Do you think you are alone? No! You are never alone because trillions of microorganisms accompany with you, on your skin, in your mouth, in every inch of your body. The human body contains many trillions of microbial cells as much as about three times of human cells. They are collectively weigh similar to weigh of your brain.

The human genome has been sequenced to reveal human biology simply from analysis the genome, but the truth is, it didn’t work out exactly as hoped. If the genome doesn’t explain everything, the pattern of microbial communities that people have in and on them is a nice alternative explanation of the variation that we see.

 

Collectively, these microorganisms are called as micro biome. Micro biome is complex microbe ecosystem that is a part of our world. Scientists still have reveal little bit of them and so much have to know. 

All we are ecosystems! Your mouth, skin and gut are home to whole communities of microscopic organisms, whose influence on your body range from digesting your food to training your immune system and they can impact your mood and behavior.

The term human micro biome refers to the complete set of genes contained in the entire collection of microorganism that live in the human body. Their genes are now thought to contribute more to human. Human micro biome is an essential organ in the human body because human body cannot function without it.

Our microbial community is called as human micro biota which is made up of bacteria, yeasts and other eukaryote, archea, fungi, protozoa and nonliving viruses.

It all starts at the very beginning

In the womb, babies are in a sterile zone with no micro biome at all. Our first microbial communities depend a lot on how we are born. Babies that come out the regular way, all of their microbes are basically like the vaginal community. Babies that delivered by C-section, all of their microbes look like skin. This might associate with some health conditions.
Continuous exposure to environment and through contact with parent, grandparents, siblings, pets which crowded with bacteria are picked by new born baby.

 

More reasons to breastfeed
Infants get several types of bacteria from their mother through breast milk and it supplys foods for other bacteria of infant. Ten present of nutrient in all breast milk can’t be digested by babies at all. They are feed on microbes in infant digestive system.

Important
They may also be doing all of things, such as educating our immune cells, like this one; teaching them the different between things they should fight off, bad bugs that might make us sick and things that aren’t a threat, like our good microbes.
When we are adults, microbes become our first line of defiance, fighting off germs that try to invade our bodies, protecting their turf while protecting our health. Scientists have discovered they can even spew out their own antibiotics.

Fingerprint
Micro biome have the potential to uniquely identify individuals, much like fingerprint as it contain enough distinguishing features to identify an individual. An unique codes for each person can be generated by looking at the microbial DNA in samples from skin, mouth, gut and vagina.
The studies suggest that micro biome sequencing may someday have utility in criminal investigation. Researches has shown that they could differentiate between small groups of individuals who had touched cell phone by matching their skin micro biota to the microbes left on the cell phone.

Differences really are skin deep
Skin microbes reveal differences about us. It differ according to age like, more oil loving bacteria present on kids under 12 than people over 12. Dogs’ owners share a microbial profile with their pets and have more diverse skin micro biome than non-dog owners. People who were antiperspirant have about 50 times fewer bacteria under their arms than people who just use soap.

Why you have morning breath
More than 1000 kinds of bacteria live in human mouth. Most of them do not harm or actively protect from infection. At right conditions they also can cause tooth decay, bad breath and gum diseases. Dominating bacteria in mouth during night and day are different.

Fecal transplant

All organisms in all environments have microbe associated with them. Beneficial microorganisms in digestive system help to absorb nutrients and digest food efficiently. But these good microorganisms are destroyed by some medical conditions and antibiotics. At that point to reintroduce them, fecal transplant is used.

Fecal transplant is known as fecal micro biota transplant (FMT) or bacterio – therapy.

What is a fecal transplant?

Feces from a healthy donor is transplanted to restore the balance of bacteria in their gut. It can help to treat gastrointestinal infections and other conditions. Some infections are cured and reduced the severity of certain gut health problems in recipient’s body by encouraging to grow healthful bacteria.

Fecal transplant donors are carefully screened to ensure that their gut and feces are healthy. They are tested for various diseases, such as hepatitis.

Donated faces can be delivered to recipient by two methods.

One is using a colonoscopy. A colonoscopy is a small, flexible tube that they can insert into the colon through the rectum. Mostly patients take sedative drugs before the procedure for not to feel any pain or discomfort.

Another approach is injecting liquid feces via an enema that using a colonoscopy.

Fecal transplanting is not a new thing. It has been practiced in ancient Chinese medicine more than 1700 years ago. In past, recipient had to drink a liquid suspension of another person’s feces. It is a highly risky technique.

Today’s fecal transplants are sterile and safe, and there is a growing body of research to support their use.

Researches are conducted on gut bacteria if they are affect overall health. If it is, fecal transplants could eventually treat a variety of conditions.

Some researches has shown that fecal transplants may eventually treat conditions such as diabetes, obesity, hay fever, arthritis.

Gut micro biome

Trillions of microbes exist inside intestine and most of them are found in a “pocket” of large intestine called cecum. Each of them plays a different role in body while most of them are extremely important for healthy but some are cause disease.

As we grow, our gut microbe begins to diversify, meaning it starts to contain many different type of microbial species. Higher the diversity of micro biome is considered good for health. Foods we eat mainly effect on diversity of gut bacteria.

Digest fiber- certain bacteria digest helps prevent weight gain, diabetes, heart disease and risk of cancers.

References

https://www.ted.com/talks/jessica_green_and_karen_guillemin_you_are_your_microbes/transcript?language=en

https://www.ted.com/talks/jonathan_eisen_meet_your_microbes?language=en

https://www.medicalnewstoday.com/articles/325128.php

Image courtesy:

Figure 1

https://pbs.twimg.com/profile_images/834701983722459137/WtAecQ1M.jpg

Figure 2

https://ars.els-cdn.com/content/image/1-s2.0-S1744165X16300129-gr1.jpg

Udara Anushika

s13278

“All mushrooms are edible;some only once in a lifetime ”

Mushroom, the conspicuous umbrella-shaped fruiting body (sporophore) of certain fungi, typically of the order Agaricales in the phylum Basidiomycota but also of some other groups. Popularly, the term mushroom is used to identify the edible sporophores; the term toadstool is often reserved for inedible or poisonous sporophores.

Mushroom is a fungus which remains underground and sends up the mushroom stem and cap which can be considered as its fruit. It is common knowledge that fungi are simple plants which neither flower nor possess chlorophyll, the green colouring matter in plants which is essential for photosynthesis. Mushrooms are a key stimulating part of vegetarian diet. It is estimated that there are over 200 varieties of mushrooms in the world. Some of the common mushroom varieties commercially marketed are: Common mushroom: The most widely available mushrooms of all the varieties are those of the agaricus family. Button mushrooms age the smallest generally sold and have not yet opened their gills. They are delicious raw, served whole in sauce or marinated. Slightly older mushrooms will have opened to reveal their gills and are more appropriate for cooking rather than raw use; when sliced they make an excellent ingredient in a stir-fry. Large open mushrooms are mainly used for stuffing. Oyster mushrooms: These are quite expensive and these have a slightly fishy flavour, a toughish texture and is used in stews, soups and casseroles. When sprinkled with lemon juice, dipped in batter, rolled in breadcrumbs and fried until golden it is said to be indistinguishable from oyster. Ceps:Highly rated and often highly expensive, the cep has a stumpy appearance and lacks the usual gills under its hamburger-bun like cap. It is delicious simply sauted in olive oil and garlic. 4. Chanterelle

Also known as Girolle, this is a gourmet mushroom whose slightly peppery apricot aroma should not be overwhelmed by strong flavours. With a fairly tough texture, it should be stewed in soya milk for about 10 minutes or alternately it makes an excellent and exotic refinement to scrambled tofu.5. Morel

Another gourmet mushroom which looks nothing like other fungi, having a honey-comb like cap. Good fried or added to casseroles, souces and soup. Alcohol should not be taken when you are consuming Morel as you may get stomach upsets Chinese Straw Mushrooms: This is available in our supermarkets as well as Chinese food stores and familiar to patrons of Chinese restaurants as an important and delicious ingredient in such dishes as fried mixed vegetables. Wooden Mushrooms: Another Chinese favourite available dried and when reconstituted with water gives a thick glutinous texture to any dish. In addition to above there are certain varieties which are not found in supermarkets namely(a) “Piduru Hathu” which grow in hagstacks and is popular among rural people and available during the paddy harvesting season .(b) “Len Hathu” .This is a popular type of mushrooms among rural folk. This mushroom has the appearance of a squirrel’s ear. When used with garlic, onions and spices and fried it is quite a tasty dish

When considering nutritional value of mushroomsMushrooms are free of cholesterol and contain small amounts of essential amino acids and B vitamins. However, their chief worth is as a specialty food of delicate, subtle flavour and agreeable texture. By fresh weight, the common commercially grown mushroom is more than 90 percent water, less than 3 percent protein, less than 5 percent carbohydrate, less than 1 percent fat, and about 1 percent mineral salts and vitamins.

In Sri Lanka too, as in other countries there are poisonous mushrooms. Poisonous mushrooms contain two types of toxins (a) phallotoxins which are heptapeptides that act quickly causing vomiting, diarrhea and abdominal pain and (b) amatoxins which are octopeptides which act on hepatocytes (liver cells) and kidney tubular cells causing kidney failure and these patients may need dialysis treatment if they are to survive. Therefore, it is dangerous to eat any type of unfamiliar mushroom. As far as I am aware the mushrooms available in our Sunday fairs, boutiques, and supermarkets are quite safe for consumption.

Mushrooms are particularly vulnerable to absorbing radioactive fallout and it would therefore be extremely prudent to avoid buying mushrooms from areas which have recently suffered from nuclear contamination 

Kisalka Athukorala

13220

Microorganisms harbor every surface of the Earth. If we resist it, we are on a wrong planet. The microbiota normally associates with the human body have an important influence on human physiology, development, immunity and nutrition. The vagina is an internal organ which is important to women. It is not sterile because of its connection with the exterior. Good bacteria that live inside the vagina of a woman are commonly known as vaginal flora. 

Healthy Vaginal Microbiome

The vaginal microbiome is unique and complex. Also, it is made up of numerous species. More than fifty different species of microbes live inside the vagina. The normal vaginal flora is dominated by various Lactobacillus species. Lactobacillus is a genus of gram positive, facultative anaerobic or microaerophilic, rod shapes, non-spore forming bacteria. Their quantity is so high as 10 000 to 100 million lactobacilli can be found per gram of vaginal fluid. Basically, these bacteria help to keep the vagina healthy and free of infection. Some strains of Lactobacillus species which help to compose a healthy vaginal ecosystem are Lactobacillus acidophilus, Lactobacillus rhamnosus and Lactobacillus reuteri. These bacteria are commonly known as Döderlin’s bacillus in honor of Albert Gustav Döderlein Sigmund who was first described their presence in the vagina in 1892.

These bacteria stick to the vaginal surface and make it more challenging for harmful bacteria to grow. They acquire nutrients from sloughed cells and granular secretion. Lactobacillus produce lactic acid, hydrogen peroxide and other substances that inhibit the growth of yeast and other unwanted organisms. Ovaries produce estradiol. Estradiol proliferates the multilayered epithelium of the vagina and also induces the glycogen loading of these cells. Vaginal epithelial cells gradually flake out in the vaginal lumen. Desquamated cells undergo a lytic process which allows the release of the glycogen contained in them.  Bacteria feed on glycogen found in vaginal mucus and in exchange emit lactic acid and in the case of some species hydrogen peroxide. Basically, they produce lactic acid by glucose anaerobic fermentation. Lactic acid has antimicrobial, antiviral and immunomodulatory properties. While acid in the vagina may sound alarming, these bacteria help to maintain the vagina at a healthy pH of around 3.5 – 4.5. This moderately acidic environment helps protect against infections. A pH level above 4.5 creates an ideal environment for unhealthy bacteria to grow. 

Hydrogen ions of lactic acid react enzymatically with oxygen to produce hydrogen peroxide. Lactic acid and hydrogen peroxide also kill harmful bacteria and viruses that can lead to infections. Sometimes Lactobacillus also adhere directly to harmful bacteria killing them and preventing from spreading. They also can produce naturally occurring antibiotics which are known as bacteriocins e.g.; lacticin and crispasin to reduce or kill other bacteria entering the vagina.  Moreover, they produce a substance that stops invading bacteria sticking to the vagina walls which prevents unhealthy bacteria invading the tissues. The vaginal microbiota is much more heterogeneous as many other species can be found inside the vagina of a healthy woman such as Staphylococcus epidermidis, Corynebacterium, Peptostreptococcus, Megaspera, Leptorichia and Eubacterium. Interestingly each woman’s own vaginal flora may be different from other women. 

Unbalanced Vaginal Microbiome      

A lack of lactobacilli and overgrowth of some other microbes can cause imbalance in the vaginal ecosystem. This imbalance can occur for a number of reasons. Mainly it could be due physiological changes and pathological changes in the vaginal environment. Alkali products used for douching, antiseptic or soap products could deeply alter the vaginal ecosystem. They remove lactic acid and healthy bacteria from the vagina. Vaginal alkalization slows down of lactobacilli metabolism and decrease in lactic acid production. Too frequent hygiene or not maintaining good hygiene habits could alter the vaginal ecosystem. Use of antibiotics may destroy not only pathogenic organisms but also healthy microbiota. Chronic stress has a negative impact on vaginal structure. Large amounts of steroids mainly cortisol can alter the growth of natural microbes and the production of lactic acid. 

The vaginal ecosystem undergoes major compositional changes throughout a woman’s life from childhood to puberty. Menstruation becomes a risk factor for the maintenance of the vaginal ecosystem. Vaginal ecosystems in less acidic because blood drag lactic acid during menstruation. Also, lactobacilli bind to the erythrocytes in the blood instead of remaining on the vaginal epithelial cells. During the coition spermatozoa can enter into the female reproductive organs. Sperms act as a powerful alkalizing agent which reduces vaginal acidity and neutralized the vagina for several hours. This can lead to colonization of alkaline tolerant pathogenic bacteria. Women who take hormonal contraceptives are susceptible to alterations of the vaginal ecosystem. The production of glycogen is disrupted due to the contraceptives with very low or no level of estradiol. Ultimately it leads to a low level of lactic acid production. During breastfeeding the amount of estrogen is relatively low. It is because the ovaries need a few weeks to recover their full functionality. This reduces the number of lactobacilli present in the vagina. When the lactobacillus population is disrupted pathogenic bacteria can take over. Usually good bacteria outnumber bad bacteria. Harmful anaerobic bacteria which can grow on the vagina are Gardnerellla vaginalis, Atopobium vaginae, Bacteroides spp., Mycoplasma hominis and Prevotella. These bacteria upset the natural balance of the vaginal ecosystem. Gardnerella vaginalis is the mostly dominates species of the disruption in the normal vaginal flora. This species is facultative anaerobic bacteria, non-spore forming and non-motile coccobacilli.

Infections in Pregnancy

Pregnant women are at increased risk of alterations of natural vaginal ecosystem because of hormonal changes during pregnancy. It could lead to a common vaginal infection known as “Bacterial Vaginosis”. Hormonal changes reduce the glycogen level in vaginal mucus. It reduces the number of healthy bacteria lacking nutrients. Ultimately it reduces the concentration of lactic acid of vaginal fluid. Reduction of healthy microbiota lead to colonization of pathogenic bacteria inside the vagina. One or more colonies can grow in unusual numbers when the vagina is unhealthy in terms of a disrupted pH balance. 

There is normally a natural balance between lactobacilli and anaerobes. Lactobacilli typically account for the majority of bacteria in the vagina. It also controls the growth of anaerobes. Anaerobes have an opportunity to grow when the lactobacilli are reduced in number. This imbalance can occur for a number of reasons including when a woman has unprotected sex with a male partner, high use of antibiotics, does not maintain good hygiene habits or douching. Bacterial vaginosis is not a sexually transmitted infection. But it is common in sexually active women. It is also the common vaginal infection in women ages 15 to 44. Approximately 10% – 30% of pregnant women will experience bacterial vaginosis during their pregnancy. Vaginal imbalance resulted in bacterial vaginosis can result various symptoms. Thin white or grey vaginal discharge, strong fishy odor, pain, itching or burning in the vagina and burning feeling when urinating. Lot of the time it causes no symptoms at all. The fish like odor associated with the discharge is a result of the chemicals that are produced by the bacteria that cause bacterial vaginosis. The pathogenic bacteria colonized in the vagina produce a number of volatile amines resulted in the fishy odor. When the blood or semen react with the bacteria, they make the odor worse in menstruation or sexual intercourse. 

Pregnancy Complications

Pregnant women who are having bacterial vaginosis have a high risk of encountering various complications during pregnancy period. Also, they have a high risk of getting various sexually transmitted infections. Pregnant women with bacterial vaginosis are more likely to have an early delivery. Premature birth is birth before 37 weeks of pregnancy. Being born too early or too small can cause many health problems in the baby. The colonization of bacteria which causes bacterial vaginosis can develop their growth in the upper genital tract, fallopian tubes and even in the uterus. These bacteria also can cause infection in the fetal membranes (amnion and chorion) and in the amniotic fluid. It will ultimately cause chorioamnionitis in pregnant women. Chorioamnionitis will set to premature rupture of the fetal membranes causing premature birth. It also has been demonstrated that certain pathogenic bacteria which causes bacterial vaginosis may translocate to the foetal placental unit. Normally foetal placental unit is associated of the interactions between the mother and conceptus to develop hormonal balance. Bacteria colonized in the foetal placental unit induce maternal or fetal response that can result in the premature birth of an infant.

Having bacterial vaginosis during pregnancy can increase risk of miscarriages. Bacteria which cause bacterial vaginosis may secrete different substances elevating vaginal or cervical levels of endotoxin, mucinase, sialidase and interleukin – α. This may stimulate the production of cytokines. It increases the risk of miscarriages. Pregnant women with bacterial vaginosis are more likely to deliver low birth weight babies. Normally babies who were born less than 2, 500 g are considered as low birth weight babies. 

The infection can travel up from the vagina to the cervix, uterus and fallopian tubes. It causes a painful condition which is known as Pelvic Inflammatory Disease. Scar tissue and collections of infected tissue may develop in fallopian tubes resulting a damage to reproductive organs. Pelvic Inflammatory Disease may cause ectopic(tubal) pregnancy. The fertilized egg is implanted in the uterus unless making its way through the fallopian tube during ectopic pregnancies. It may also cause life threatening bleeding. Infertility is the inability to become pregnant. Pelvic Inflammatory Disease can damage reproductive organs resulting infertility. It also may cause chronic pelvic pain. Tubo ovarian abscess is arising by collecting pus in uterine tubes and ovaries due to Pelvic Inflammatory Disease. These harmful bacteria can even cause endometritis, chorioamnionitis and neonatal meningitis. Bacterial vaginosis put a high risk for infections after surgeries affecting the reproductive system. These include abortions, hysterectomies and cesarean deliveries. And it also has a greater chance of developing another type of infection after delivery. Bacterial vaginosis increases the risk of getting sexually transmitted infections including chlamydia and herpes simplex virus because of the already unbalanced ecosystem of the vagina. 

Urinary tract infections are also caused by bacteria vaginosis adversely leading to infections in kidneys.  Normally when the baby comes through the birth canal during a vaginal delivery the new born baby is colonized by microbiota in the mother’s vaginal fluid. It helps to protect from various diseases in the new born environment. When the maternal microbiota gets disrupted with bacterial vaginosis infant encounters an unhealthy pathogenic bacteria. It may depress the immunity in the new born baby causing various health problems.  

Most commonly bacterial vaginosis is treated with antibiotics. These antibiotics are given orally or as vaginal gels. Interestingly certain studies show that probiotic therapy may increase the colonization of healthy bacteria in the vagina such as Lactobacillus. Collectively the vaginal flora has an important impact on women’s health as well as that of their new born babies. The composition of the vaginal microbiota depends on age, menstruation, hormonal fluctuations, sexual behaviors and also use of drug such as probiotics and antibiotics. The imbalance in the composition of the vaginal microbiota can lead to dysbiosis mostly in pregnant women. Thus, it essential to keep the vaginal ecosystem healthy to get rid of the complications.   

References

• https://www.medicalnewstoday.com/articles/322210.php
• https://americanpregnancy.org/pregnancy-complications/bacterial-vaginosis-during-pregnancy/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940187/
• https://academic.oup.com/epirev/article/24/2/102/535045 

Image Courtesy

1. https://cdn.newsfirst.lk/english-uploads/2019/08/ecd21206-pregnant.jpg – Featured Image

2.https://www.researchgate.net/publication/276526216/figure/fig1/AS:669019057168386@1536517981023/Vaginal-Lactobacillus-acidophilus-or-Doederlein-bacillus.png – Figure 1

3.https://www.news-medical.net/image.axd?picture=2019%2F10%2Fshutterstock_1174108663_6b5ec65d1212440c8894f84d83f31b23-620×480.jpg – Figure 2

4.https://cdn2.momjunction.com/wp-content/uploads/2015/12/Intra-amniotic-Infection-1-01-1-1.jpg – Figure 3

Lakma Rathuge

s13266

Industrial microbiology is a branch of biotechnology that applies microbial sciences to create industrial products in mass quantities. Numerous microorganisms are used within industrial microbiology; these include naturally occurring organisms, laboratory selected mutants or genetically modified organisms (GMOs). Currently, the debate of use of genetically modified organism (GMOs) in industry is gaining both momentum, with more and more supporters on both sides. However, the use of microorganisms at an industrial level is became major in today’s society. In industry, final products from microorganisms may be; microbial cells (living or dead), microbial biomass, components of microbial cells, microbial metabolites, intercellular or extracellular enzymes, chemicals produced by the microbes, modified compounds that has been microbiologically transformed or recombinant products through the DNA recombinant technology.

These microorganisms are used extensively to provide a vast range of products and services, because they have proved to be particularly useful because of the ease of their mass cultivation, speed of growth, use of cheap substrates (which in many cases are wastes) and the diversity of potential products. During their metabolism, primary metabolites are consumed for proper growth as essentials and they produced secondary metabolites at the end or near the stationary phase of growth. Secondary metabolites do not play a major role in growth and development and reproduction directly. But these metabolites can be used industrial microbiology to obtain economically demand products such as amino acids, develop vaccines and antibiotics and isolate chemicals necessary for organic synthesis. Any process mediated by or involving microorganisms in which a product of economic value is obtained is called fermentation. Traditional fermentations were originally performed by a mixture of wild microorganisms emanating from the raw materials or the local environment (ex: some food and alcoholic beverage fermentation). Developed fermentation processes mostly use monocultures which the specific microorganism employed were often isolated from the natural environment. Alternatively, suitable microorganisms are acquired from culture collections, because in most cases, regulatory considerations are major importance when choosing microorganisms for industrial use. Fermentation industries often prefer to use established GRAS (generally regarded as safe) microorganisms, particularly for the manufacture of food products and ingredients. 

Examples of microorganisms classified as GRAS (generally regarded as safe)

Bacteria

          Bacillus subtilis

           Lactobacillus bulgaricus

          Lactobacillus lactis

          Leuconostoc oenos

Yeast

         Candida utilis

         Kluyveromyces marxianus

         Kluyveromyces marxianus

         Saccharomyces cerevisiae

Filamentous fungi

         Aspergillus utilis

         Aspergillus oryzae

         Mucor javanicus

         Penicillium requeforti

* Normally, these microorganisms require no further testing if used under acceptable cultivation conditions.

Table 01: Examples of industrial fermentation products and their producer microorganisms.

Industrial microbiology deals with screening, exploitation of microorganisms, improvement and management of microorganism for the production of various useful end products on a large scale. It involves processes and products that have major importance in the field of economic, environmental and social importance. Major aspects in industrial microbiology are production of valuable microbial products via fermentation processes. The market size of industrial microbiology is growing at a large scale, because the market analyses competitive developments such as expansions, agreements, new product launches/research, and acquisitions in the market.

Further improvement is a vital part of process development in most fermentation industries. It provides a means by which production costs can be reduced through increases in productivity or reduction of manufacturing cost. The improvement process may target rapid growth of the population of microorganisms, genetic stability, non-toxicity to human, large cell size for easy removal from the culture fluid, ability to use cheaper substrate, modification of submerged morphology, elimination of the industrial wastes, bioremediation, catabolite derepression, phosphate deregulation, metabolite resistance and production of additional enzymes etc.

However, improved product’s quality and safety must be approved prior to approval for marketing, any new food or health care products that is to be used by humans and domestic or farm animals must be thoroughly tested. This involves aspects of safety and efficacy and required specifications for purity and activity. Product licenses are granted only after the product has passed all the requirements of the regulatory system.

Rochana Piyumal

s13263

Everything in our planet can be basically divided in to two sub section as living and non-living things. Animals, plants and microorganism belongs to living category. Except those tree things, rest goes to the non-living category. Diversity of living being is higher. Among three different living types, microorganisms are more specific because they are the smallest organism types in the world. Microorganism can be divided into sub sectors as bacteria, fungi, algae, protozoa and virus. Microorganisms may have prokaryotic or eukaryotic cell composition. Some are cellular whilst some form multicellular types. They have successfully distributed all around the world. They can live any places in the world even in areas with extreme environmental conditions such as higher temperature (Dessert) and lower temperature (Poles). They have developed different cellular mechanisms to adopt those conditions.

Microbiology is the scientific study of microorganisms. As mentioned in the previous paragraph, microorganism have different and unique functions that make sure their survival in the ecosystem. Due to those different functions, they have become a useful factor in each ecosystem. Microorganisms have different way of interaction with other living organisms in the same environment. Some of them may cause disease (Pathogenic organism) to the other living forms including animals and plant whilst some of them act against those disease-causing organism (Antimicrobial activity). Another set can make mutualistic relationship with other living organism. For example, rhizobium bacteria can fix atmospheric N inside the legume plants. Plant fulfill part of their N requirement through this symbiotic relationship. Microorganism takes food and place to live from host plant. Also, some microbial functions can be used for beneficial productions such as fermentation (alcohol, vinegar and dairy productions), antibiotic production, food production, wastewater treatment, creating biofuels and a wide range of chemicals and enzymes. 

Study of different microbial functions in scientific way to produce novel product is called as applied microbiology. Under this field, different subfields such as biotechnology, agriculture, medicine, food microbiology and bioremediation can be seen. Researchers in each sector conduct experiments to develop better product or mechanisms. For example, people who are doing researches in medicine, try to develop new antibiotics to replace current antibiotics or add more powerful antibiotics. Also, in agriculture sector, some researches are conducted to find reduce chemical fertilizer use through biofertilizer (applying microorganisms which can be the source for providing nutrients to the plant).

In this article, we focus on microorganism related to medicine specially drug discovery which is one of most important sectors in the medicine. Different products obtained from microbes are already commercially available. Those products help to maintain health and well being human throughout the world. Antibiotics, enzymes, vitamins are some extracted products from different microbes used in medicinal sectors. In addition, some primary metabolites such as amino acids, vitamins and nucleotides are also used in medical sector. Most importantly, their secondary metabolites can use for producing pharmaceuticals for different diseases. Drugs derived from bacterial secondary metabolites are in manifold use, for example in diagnosis, mitigation, or in the treatment, or prevention of a disease or relief of discomfort. Today, half of the available pharmaceuticals have been produced from microbial secondary metabolites. 

The first use of microbial derived drug goes back more than 80 years. In 1929, Alxander fleming discovered antimicrobial compound called as penicillin. He observed growth inhibition of his petri dish inoculated with Staphylococcus aureus from mold. This mold can secrete compound to the petri dish that prevent growth of bacteria. Later, this mold was identified as fungal growth and organism as Penicillium notatum. Therefore, this drug was named as penicillin. This discovery was able to save millions of lives. Hence this drug is also identified as “wonder drug”.  Alxander fleming won Nobel prize for this amazing discovery as well. This drug is still used in medical sector as front line antibiotic drug. After fleming’s discovery, researchers focused on discovery of drugs from different microorganisms. As result of this effort, many antibiotics secreted from microorganism such as streptomycin, cholrophenicol etc. are available in medical sector. 

Environmental microbes are major source of drug discovery. Researches have been conducted under different sectors such as antibiotics, anticancer, antitumor, immunosuppressants etc. Microorganisms in natural environment were isolated and tested under the different categories mentioned above to identify positive results. If the microbial product can give positive result, it may have a chance to develop as a drug. However, each successive compound is not used as drug. It should also be suitable to human. Therefore, few of identified compound comes to the end and becomes drugs. Also, most of these discoveries have been done using cultivable environmental microorganisms (1%). Since, small portion of microbes have been used so far, drug discovery from microbes is still a good source. With the technological development, drug discovery from microbes is expanding furthermore. Isolation of secondary metabolites from uncultivable microorganisms is becoming popular now a days. 

Over one million of natural compounds have been discovered so far. Among them, 5% of compounds have a microbial origin. Also, among natural compounds, approximately 20-25% have shown biological activity. Among biological active compounds. Over 10% of compounds have been isolated from microorganism. More than 22,500 biologically active compounds were isolated from microorganisms. Bacteria, fungi and actinomycetes are main microorganism types. Their contribution divides as 45% from actinomycetes, 38% from fungi and 17% from bacteria. Production of antimicrobial compounds and treatment for serious disease from microorganisms have been increased with the time. Also developing resistance against antimicrobial compound by the pathogens is becoming a promising problem now days. Use of antibiotics without doctor prescription is major reason for that. Therefore, more researches are required to replace those antibiotics. 

An antibiotic are chemical compounds released by one microorganism and inhibit the growth of another microorganism. Antibiotics is also identified as antimicrobial substances which is widely used medical sector for prevention of pathogenic infections. They may either kill or inhibit the growth of bacteria. Before discovered the first antimicrobial drug “Penicillin”, people were died even from minor infections such as strep throat. At that time, doing surgery was not easy and it was risky due higher chance of getting infected. With antibiotics, human lives are safer. Surgeries are not risky.Three main process are used during the modern antibiotic production from microorganism as natural fermentation, semi synthetic and synthetic.       

Antibiotic production is an important microbial process for human health. However, they do not produce antimicrobial compounds for humans. They produce those compounds for their safety. Microbes live on earth for several billion years. During the time, microbes evolve to produce various compounds for their safety or protect from the competitive other organisms. Also, the other organisms have evolved to resist those antimicrobial compounds. It is a natural concept. Once one organism gets ability to produce compound which can control the others growth and make them prominent, rest of the organism start to resist it. For example, more than 70% of bacteria can produce biofilm. Biofilm is a protective cover created by the pathogenic organism which covers from antimicrobial compounds. Since the biofilm production of the bacteria, they are able to resist at least one common antimicrobial drug. Some biofilm works for different antimicrobial compounds. Biofilm can grow on different places such as wounds, scar tissues and medical implants or devices, such as joint prostheses, spinal instrumentations, catheters, vascular prosthetic grafts and heart valves. Therefore, increasing resistance against available antibiotics in medical sector is a normal incident. However, the problem is that some pathogenic microbes have developed multidrug resistance. Hence, scientists should be developed new antibiotics in higher rates. Otherwise, it may be caused to increase the risk of human health same as the early stages. Following table show some antibiotics produced from microorganism. 

Antibiotic	Producer organism
Penicillin	Penicillium chrysogenum
Cephalosporin	Cephalosporium acremonium
Griseofulvin	Penicillium griseofulvum
Bacitracin	Bacillus subtilis
Polymyxin B	Bacillus polymyxa
Amphotericin B	Streptomyces nodosus
Erythromycin	treptomyces erythreus
Neomycin	Streptomyces fradiae
Streptomycin	Streptomyces griseus
Tetracycline	Streptomyces rimosus
Vancomycin	Streptomyces orientalis
Gentamicin	Micromonospora purpurea
Rifamycin	Streptomyces mediterranei

Acute respiratory infections, diarrhea, tuberculosis, HIV, measles and malaria are major desease types caused to more than 90% of death in the developing world. In developing and developed countries together, reparatory track infections are the major reason for death. In developing countries, seven respiratory tract infecting microorganism are mainly responsible for that. They are Bordetella pertussis, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Mycoplasma pneumoniae, Chlamydophila pneumoniae and Chlamydia trachomatis. Also, major respiratory viral infections are respiratory syncytial virus, human parainfluenza viruses 1 and 3, influenza viruses A and B, as well as some adenoviruses. Due those infections, 17 millions of peoples died per year. In addition, this can be a major impact on economy and society of each country. Countries has to spend more money on health sector. Also, it is hard to take maximum contribution from people to the development process. Hence, these microbial infectious diseases can be done a dramatic loss to the country in different ways such as economic growth, development and prosperity. Different factors can be caused for emerging infectious disease in each country. Ecological changes can be a good reason for emerging infectious disease. Some change in environment may promote the increasing the number and spreading of the pathogenic microbes. Changes in human demographics and behavior can be another reason for promoting infectious disease. International travel can also increase the chance of getting infectious disease. Due to different environmental condition in different areas may be a reason to change person immunity. Low immunity has higher chance of getting disease. Break down of public health measures can lead people to get infected. Therefore, new drugs discovery from different resources including microorganisms is most important scientific process in the world. For this process, microorganisms can be actively involved due to its potential.  

References

https://www.nature.com/articles/ja200816

https://microbiologysociety.org/event/society-events-and-meetings/antimicrobial-drug-discovery-from-traditional-and-historical-medicine-1.html

https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.12388

https://www.researchgate.net/publication/23766836_Demain_A_L_Sanchez_S_Microbial_drug_discovery_80_years_of_progress_J_Antibiot_Tokyo_62_5-16

https://academic.oup.com/jac/article/73/6/1452/4847822

Image Courtesy

https://alchetron.com/Streptomyces-nodosus

https://www.carolina.com/bacteria/bacillus-subtilis-living-tube/154921.pr –

https://www.bustmold.com/resources/mold-library/penicillium-chrysogenum/

https://media.nature.com/w700/magazine-assets/d41586-018-02477-1/d41586-018-02477-1_15510426.jpg

Divya Munasinghe

s13257

Food is the important basic substance for human being which provides the nutrients for survival. Food processing is the process of making food from the different raw materials through physical and chemical processes. Household and industrial food productions are the two important source of prepared food.

Microorganisms are very tiny in size. They are not visible to the naked eye. Microorganisms are present in all type of environmental sources like soil, air, water, animal body and plant etc.

Some of the microorganisms are involved in the food processing and preservation at household and industrial food production.

Nature uses microorganisms to carry out fermentation processes, and for thousands of years mankind has used yeasts, moulds and bacteria to make food products such as bread, beer, wine, vinegar, yoghurt and cheese, as well as fermented fish, meat and vegetables.

Fermentation is one of the oldest transformation and preservation techniques for food. This biological process allows not only the preservation of food but also improves its nutritional and organoleptic qualities (relating to the senses; taste, sight, smell, touch). A well conducted fermentation will favour useful flora, to the detriment of undesirable flora in order to prevent spoilage and promote taste and texture.

Figure 1

A bit of history

The first realisation that microorganisms were involved in food production processes was in 1837, when scientists discovered the role of yeast in an alcoholic fermentation

Later, when the world renowned French chemist and biologist Louis Pasteur was trying to explain what happened during the production of beer and vinegar in the 1860es, he found that microorganisms were responsible.

However, it wasn’t until after the Second World War that the food industry began to develop the biotechnological techniques we rely on today to produce a wide variety of better, safer foods under controlled conditions.

Do you know?

Currently, more than 3500 traditionally fermented foods exist in the world. They are of animal or vegetable origin and are part of our daily life. Alcoholic drinks are not the only fermented drinks; cocoa beans, coffee grains and tea leaves are fermented after harvest in order to develop their typical flavor profiles.

Moreover, fermented products have geographical specificities:

• in Europe, cheese and bread are widely consumed
• in Africa, products manufactured from fermented manioc play a key role in the diet 
• in Asia, products derived from soy or fish are consumed on a daily basis

Production of microbial cultures in the dairy industry

Since ancient times, dairy products have been part of human diet. These serve as good source of calcium, vitamin D, proteins and other essential nutrients. These products also provide 

Phosphorus, potassium, magnesium, and various vitamins viz. vitamin A (retinols), vitamin B12 (cyanocobalamin), and riboflavin. Various fermented dairy products are prepared using different microbial strains. Microbes ferment the carbohydrates present in milk, which is mainly lactose to lactic acid and some other products. The acid precipitates the proteins in the milk; therefore fermented products are usually of thicker consistency than milk. The high acidity and low pH hinders the growth of other bacteria including pathogens. The fermentation of milk provided a simple way to increase its shelf-life while improving its safety. Humans learned to control fermentation processes from the initial accidental events in fermentation. This learning of controlled fermentation of milk in domestic practices gave rise to a diverse dairy products influenced by habits of different ethnicities, geographical environments and type of dairy farming. 

Now, a huge variety of fermented dairy products are available for consumers. Although a small proportion of these products are homemade, most of them are produced industrially. The production of fermented products is economically important in many countries. As the requirement of fermented products is increasing day by day, and in many countries dairy industries are contributing in economic growth. The first example of fermented milk was presumably produced accidentally by nomads. This milk turned sour and coagulated under the influence of certain microorganisms. By luck it was having harmless, acidifying type and non-toxin-producing bacteria.

Various types of fermented milks and derived products have been developed in all parts of the world each with its own characteristic history. Their nature depends very much on the type of milk used, on the pre-treatment of the milk, on the temperature (climate), conditions of fermentation and on the subsequent technological treatments. Most commonly used dairy products include curd, yogurt, cheese, kefir and kumis. 

Curd

Curd is made by curdling or coagulating the milk. This can be done by mixing edible acidic substances in to the milk, such as lemon juice or vinegar. By adding these substances to the milk, it will curdle the milk and separate into two parts. 

The liquid part is the whey and the solid milk is the curd. The whey contains whey proteins of the milk, whereas the curds are the milk proteins or casein. Sometimes old milk might get soured and is separated without any added acidic substance. This happens because raw milk contains Lactobacillus. Lactobacillus is a genus of bacteria that converts sugars into lactic acid by means of fermentation. Milk contains a sugar called as lactose, a disaccharide (compound sugar) having β-1, 4- glycosidic bond between galactose and glucose. Lactobacillus converts lactose of the milk into lactic acid which imparts the sour taste to curd.

Yogurt

Yogurt is most commonly used dairy product. It is prepared by heating the milk up to nearly 80°C in order to kill any additional bacteria that may be present and to denature milk proteins. The milk is then allowed to cool slowly to around 45°C, and thereafter, it is inoculated with a bacteria, and is allowed to ferment at room temperature. The bacteria used are Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarius subsp. thermophilus. If bacteria is not available, then a spoonful of yogurt can also be used as it contains bacteria. Probiotic bacteria like Streptococcus thermophilus, Lactobacillus acidophilus and bifidobacteria can also be used for the production of yogurt and it is commonly referred as bioyogurt. Many evidences indicated that consumption of ‘probiotic’ microorganisms helps in maintaining a favorable microbial profile and is resulted in several therapeutic benefits.

In industry, large quantity of yogurt is produced that is affected by number of factors viz. choice of milk, milk standardization, milk additives, de-aeration, homogenization and heat-treatment, choice of culture and plant design. The milk used for yogurt production must be of the highest bacteriological quality. It must have a low content of bacteria and substances which may impede the development of the yogurt culture. It must not contain antibiotics, bacteriophages or sterilizing agents. The fat and dry solids contents of the milk must be standardized and additives like sweetener or sugar and stabilizer can be used. The air content of the milk should be as low as possible so that viscosity and stability of the yogurt is improved. To assure uniform distribution of milk fat and to prevent creaming during incubation period, milk is homogenized. The milk is heated before inoculation to improve its properties as a substrate for the bacterial culture. Many types of yogurt cultures are available that can be selected based on the type of yogurt production. The plant layout is very important as the selection and dimensions of pipes, valves, pumps, coolers etc affects the production. 

Cheese

Cheese is a fermented milk product and historically serving as a mean of preserving milk. Cheese making occurs in three main stages: In the first stage, milk is moulded into solid curd and liquid whey by the coagulation of the milk protein, casein. The coagulation of casein is done through two complementary methods: acidification and proteolysis. Acidification occurs when lactic acid bacteria ferment the disaccharide lactose to produce lactic acid. Originally, it can be done by naturally occurring lactic acid bacteria in the milk but today, dairy industries usually standardize the process by the addition of domesticated bacterial cultures, including strains of Lactococcus lactis, Streptococcus thermophilus and Lactobacillus sp. The production of acid by these bacteria causes casein to coagulate slowly. This process is often assisted by the addition of the enzyme, chymosin (active ingredient in rennet). Chymosin removes negatively charged portion of casein that results in rapid aggregation of casein proteins.

In the second stage, curd is separated containing the casein and milk fat from the whey. Depending on the type of cheese, the curd can be heated, salted, pressed and is moulded into various shapes and sizes. Cheese can be eaten afresh at this point, or can be left to age in a damp, cool place. During the aging stage, cheese is truly transformed from fresh cheese into the myriad flavours, aromas, and textures of mature cheese. As a normal part of the aging process, cultures and lactic acid bacteria continue to grow and metabolize the interior of the cheese, while the surface of a cheese is colonized by bacteria and fungi that form a multispecies bio-film called as ‘rind’ of the cheese. 

Diversity in the cheese flavor, smell and texture is because of different microbes. Cheese flavor is associated with the amino acid catabolism. The ability of lactic acid bacteria and other cheese microorganisms to degrade amino acids to aroma compounds is highly strain dependent. These are equipped with enzyme systems for using amino acids in their metabolism. Different amino acids catabolism gives different flavors’ as follows:

1.  Branched-chain amino acids (Leu, Ile, Val) are converted to malty, fruity and sweaty flavors.
2. Aromatic amino acids (Phe, Tyr, Trp) produce floral, chemical and faecal flavors.
3.  Aspartic acid (Asp) is catabolised into buttery flavors. 
4. Sulphur containing amino acids (Met, Cys) are transferred to boiled cabbage, meaty and garlic flavors.

Kefir

Kefir is a fermented milk beverage which has its ancient origin in Eastern Europe. This light alcoholic beverage is prepared by inoculation of raw milk with irregularly shaped, gelatinous white/yellow grain called kefir grains. These Kefir grains have varying and complex microbial composition that includes species of yeasts, lactic acid bacteria, acetic acid bacteria and mycelial fungi. Lactic acid bacteria included in kefir are Lactobacillus fermentum, Lactobacillus acidophilus, Lactobacillus helveticus, Lactobacillus casei, Lactobacillus kefiri, Leuconostoc mesenteroides, Lactobacillus parakefiri, Lactobacillus brevis and Lactococcus lactis. Acetic acid bacteria include Acetobacter aceti and Acetobacter rasens; yeasts include Candida lambica, Kluyveromyces marxianus, Saccharomyces exiguous and Torula kefir. The population composition may differ based on the origin of grain or the method and substrate by which grains have been cultured. A symbiotic relationship exists between the microbes present inthe Kefir grains and it has been shown that there are specific species that always occur in the grains.

Kumis (Koumiss)

Kumis and kefir are similar dairy products but kumis is produced from a liquid starter culture as compared to solid kefir “grains”. It has mild alcohol content as compared to kefir because mare’s milk contains more sugars than other milks. It is very popular in Kirgizstan, Mongolia, Kazakhstan and some regions of Russia and Bulgaria. It is usually made from, area’s milk by spontaneous fermentation of lactose to lactic acid and alcohol.

Figure 2

Production of microbial cultures in meat industry

Meat starter cultures are used to make dried, fermented products such as salami, pepperoni, chorizo and dried ham. Lactic bacteria develop the flavour and colour of the products. In addition, a wide variety of moulds are use to ripen the surface of sausages, preserving the natural quality of the product and controlling the development of flavour.

Figure 3

Production of microbial cultures in wine industry

Yeasts are responsible for the fermentation process which produces alcohol in wine. However, lactic bacteria also play an important role, as they convert the unstable malic acid that is naturally present in wine into the stable lactic acid. This conversion gives the stability that is characteristic of high-quality wines that improve on storage.

Winemaking is a microbiological process involving a very complex system. The nature of the micro-organisms that inhabit grape must—along with the must’s chemical composition and temperature—influence the parameters that affect wine quality. Yeast and bacterial populations in wine are varied and variable. During alcoholic fermentation, different yeast species successively dominate, while others remain in the minority or disappear. The four fundamental parameters of pH, alcohol, temperature and CO2 determine the evolution of indigenous microbial populations, which may be monitored by winemakers from the beginning to the end of alcoholic fermentation. Interactions among microorganisms are key factors in fermentation, but those interactions are difficult to evaluate. The use of starter cultures that massively increase yeast population is a convenient and sure way to master the microbiological composition of the system. The addition of yeasts has become a classic step in winemaking that has gotten more refined as different strains become available. Today, this step is becoming more complex with the arrival of non-Saccharomyces yeast species. The addition of commercially available wine LAB is becoming more established as the available starter cultures become more reliable.

Figure 4

Production of microbial cultures in health food industry

Lactic bacteria are used in many different tablets and capsules sold as supplements in the health food industry. Our hectic modern lifestyles often lead to an imbalance in the intestinal flora; travel and medical treatment are two of the major culprits. By taking supplements containing lactic bacteria, this balance can be restored, improving the quality of life.

Image Courtesy:

Figure 1 – https://effca.org/microbial-cultures/food-production/ 

Figure 2 – https://www.labmanager.com/news/2016/08/milk-truck-microbial-study-aims-to-    improve-dairy-food-safety-and-quality#.XiGZwsgzZPY 

Figure 3 – https://www.thermofisher.com/blog/food/microbiology-of-red-meat/ 

Figure 4 – https://www.smithsonianmag.com/science-nature/wine-gets-some-its-unique-flavors-regional-microbes-180956729/ 

Featured Image – https://effca.org/_images/pages/2.jpg

Judy Mathushika Manohitharaj

s13252

Coronaviruses are a group of viruses that cause diseases in mammals and birds. Coronaviruses are viruses in the subfamily Orthocoronavirinae in the family Coronaviridae, in the order Nidovirales. Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome and with a nucleocapsid of helical symmetry. The genomic size of coronaviruses ranges from approximately 26 to 32 kilobases, the largest for an RNA virus.

The name “coronavirus” is derived from the Latin corona, meaning crown or halo, which refers to the characteristic appearance of the virus particles virions by electron microscopy, which have a fringe of large, bulbous surface projections creating an image reminiscent of a royal crown or of the solar corona. This morphology is created by the viral spike (S) peplomers, which are proteins that populate the surface of the virus and determine host tropism. 

Proteins that contribute to the overall structure of all coronaviruses are the spike (S), envelope (E), membrane (M) and nucleocapsid (N). In the specific case of the SARS coronavirus, a defined receptor-binding domain on S mediates the attachment of the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). Some coronaviruses (specifically the members of Betacoronavirus subgroup A) also have a shorter spike-like protein called hemagglutinin esterase (HE). 

Following the entry of this virus into the cell, the virus particle is uncoated and the RNA genome is deposited into the cytoplasm.

The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail. This allows the RNA to attach to ribosomes for translation.

Coronaviruses also have a protein known as a replicase encoded in its genome which allows the RNA viral genome to be transcribed into new RNA copies using the host cell’s machinery. The replicase is the first protein to be made; once the gene encoding the replicase is translated, the translation is stopped by a stop codon. This is known as a nested transcript. When the mRNA transcript only encodes one gene, it is monocistronic. A coronavirus non-structural protein provides extra fidelity to replication because it confers a proofreading function, which is lacking in RNA-dependent RNA polymerase enzymes alone.

The RNA genome is replicated and a long polyprotein is formed, where all of the proteins are attached. Coronaviruses have a non-structural protein  a protease  which is able to separate the proteins in the chain. This is a form of genetic economy for the virus, allowing it to encode the greatest number of genes in a small number of nucleotides. 

Coronaviruses are believed to cause a significant percentage of all common colds in human adults and children. Coronaviruses cause colds with major symptoms, e.g. fever, throat swollen adenoids, in humans primarily in the winter and early spring seasons. Coronaviruses can cause pneumonia, either direct viral pneumonia or a secondary bacterial pneumonia and they can also cause bronchitis, either direct viral bronchitis or a secondary bacterial bronchitis. The much publicized human coronavirus discovered in 2003, SARS-CoV which causes severe acute respiratory syndrome (SARS), has a unique pathogenesis because it causes both upper and lower respiratory tract infections. 

There are seven strains of human coronaviruses: Human coronavirus 229E (HCoV-229E), Human coronavirus OC43 (HCoV-OC43), SARS-CoV ,Human coronavirus NL63 (HCoV-NL63, New Haven coronavirus), Human coronavirus HKU1, Middle East respiratory syndrome coronavirus (MERS-CoV), previously known as novel coronavirus 2012 and HCoV-EMC, Novel coronavirus (2019-nCoV), also known as Wuhan pneumonia or Wuhan coronavirus. (‘Novel’ in this case means newly discovered, or newly originated, and is a placeholder name.) 

In December 2019 a pneumonia outbreak was  reported in Wuhan, China. On 31 December 2019, the outbreak was traced to a novel strain of coronavirus, which was labeled as 2019-nCoV by the World Health Organization (WHO). It is a novel coronavirus – that is to say, a member of the coronavirus family that has never been encountered before. Like other coronaviruses, it has come from animals. Many of those infected either worked or frequently shopped in the Huanan seafood wholesale market in the center of the Chinese city, which also sold live and newly slaughtered animals. New and troubling viruses usually originate in animal hosts. Ebola and flu are examples. 

Researchers are racing to make a Coronavirus vaccine. New technology and better coordination have sped up development. But a coronavirus vaccine is still months and most likely years away.

Historically, vaccines have been one of the greatest public health tools to prevent disease. But even as new technology, advancements in genomics and improved global coordination have allowed researchers to move at unprecedented speed, vaccine development remains an expensive and risky process. It takes months and even years because the vaccines must undergo extensive testing in animals and humans. In the best case, it takes at least a year and most likely longer for any vaccine to become available to the public.

Vaccines may not help in the very early stages of an outbreak, but if is able to develop vaccines in time, they will be an asset later. So till today no medicine has been found to cure the vast outbreak of  Coronavirus.

Figure 1: https://upload.wikimedia.org/wikipedia/commons/thumb/7/78/Coronaviruses_004_lores.jpg/800px-Coronaviruses_004_lores.jpg

Figure 2: https://static01.nyt.com/images/2020/01/28/science/28VIRUS-VACCINE1/28VIRUS-VACCINE1-jumbo.jpg?quality=90&auto=webp

Teena Samarathunga

s13299

 We all should have heard of the word Micro-organisms once in our life. So,who are these personnels? They are a group of organisms like us, but hide themselves in the world invisible to humans.Yes,they are invisible to our naked eye. I can hear your minds asking me, so,how did you see them ? Micro organisms are seen through microscopes,either light microscope or an electron microscope.

There is a wide variety of organisms under the category. The five major categories under the group micro organisms are; bacteria, fungi, certain algal species, protozoans, and viruses.

They occupy a wide range of area within the ecosystems occupied by us, and they consume a lot of resources consumed by us too.Even though, there are many resources that they should need for survival,the major resource that they compete with us are mainly the food , but they never demand for the fres food as we do! They live a simple life,even by feeding on the left overs and the spoilt food that are kept aside by us.

Yes,they feed on our food,and either they impose a desirable effect to our food or they readily spoil our food.The specific groups of micro organisms readily do their respective duty. 

Hence,from ancient times,micro organisms have been used in our daily life for various uses like, composting, in sewage treatment,as insecticides etc., These micro organisms are also successfully exploted in producing various kinds of food too.

In the ancient times, there are no records that these microbes were identified and recorded before usage, but ,their effects on the food were individualistic,and the ancient men were skilled in getting the use of the correct microbes for the correct work.

These observations and their effects were later identified to be better useful in food processing industry also.

Dairy products

Dairy products are the products produced from Milk. Milk is processed using different chemical reactions and they are enhanced using different microbes.Thus,these micro organisms become effective in giving commercial value to the milk products.

Yoghurt

Yoghurt is a favourite dessert of most of us;especially the kids.Bacteria such as Lactobacillus bulgaricus  and Streptococcus thermophilus  are exploited in the production of Yoghurt. Milk posesses a compound called Lactose within it.The microbes first convert this lactose to lactic acid.As this creates an acidic environment within the milk, which stops the functioning of Streptococcus thermophilus and then initiates the functioning of Lactobacillus bulgaricus . 

Simply, the formation of this acid clots the milk and solidifies the proteins of milk,thus completing the production of yoghurt,but there are various researches carried out in identifying the best temperatures for these  bacteria to do their work optimally.Not only temperature other environmental factors and parameters are also considered and tested .As a result,there are new flavours and new varieties of yoghurts developed with commercially desired properties too.

Yoghurts a few years back could only be stored in a retail shop for 3 or 4 days.But , nowadays,they are kept for almost a month or more.

Curd production

Curd production too invloves a lot of micro organisms and their properties.

Curd also involves the same procedure as above.

You should have seen in various Television shows,that they prepare curd and yoghurt at domestic levels too.have you imagined where does these micro organisms come from ,when they are prepared at home ? There is an important step in the preparation;that is  to add a previously prepared culture(which is usually an already available curd sample or a yoghurt sample)

Other important food and beverages used in producing microbes are

Bakery products

Bakery products are usually prepared using wheat flour.  Yeast is a type of fungi.They are added to the flour dough prepared to make the product.Yeast respire,like us using the flour and releases Carbon dioxide gas.

The fermentation process made by the yeast gives a specific taste to the product as well as it gives the rised form to the product due to the release of carbon dioxide gas.These are bubble holes you see in your dinner bread.

Beverages

Wine production

Wine is made from grapes or other fruit. The grapes are first cleaned of leaves and stems and the fruit is crushed into must that is ready for fermentation. The yeasts used for the fermentation grow a film on the fruit or in the environment. These wild strains play an important role in the final properties of the drink. However, cultivated strains of Saccharomyces cerevisiae are often added to improve the consistency of the final product. There are hundreds of commercially available yeast strains for wine fermentation.

In the fermentation process, energy that is converted to heat is produced as well. It is important to keep the temperature in the fermentation vessel lower than 40ºC to keep the yeasts alive. To improve yeast growth, additional nutrients, like diammonium phosphate, are sometimes added in the fermentation step.

When making red wine, there is an additional fermentation step after alcoholic fermentation. Malic acid, naturally present in grape juice, can be converted to lactic acid by lactic acid bacteria naturally found in wineries or added artificially.

Beer production

Beer is the most consumed alcoholic beverage in the world. It is made most often of malted barley and malted wheat. Sometimes a mixture of starch sources can be used, such as rice. Unmalted maize can be added to the barley or wheat to lower cost.

 Potatoes, millet and other foods high in starch are used in different places in the world as the primary carbohydrate source.

The process of making beer is called brewing. It includes breaking the starch in the grains into a sugary liquid, called wort, and fermenting the sugars in the wort into alcohol and carbon dioxide by yeasts. Two main species are used in the fermentation process: Saccharomyces cerevisiae (top-fermenting, since it forms foam on top of the wort) and Saccharomyces uvarum (bottom-fermenting). Top-fermenting yeasts are used to produce ale, while bottom-fermenting produce lagers. The temperature used for top-fermenting (15-24ºC) leads to the production of a lot of esters and flavor products that give beer a fruity taste. Hops are added to introduce a bitter taste and to serve as a preservative.

Brewer’s yeasts are very rich in essential minerals and B vitamins, with the exception of vitamin B12. Beer brewing in modern days is performed by added pure cultures of the desired yeast species to the wort. Additional yeasts species that are used in making beer are Dekkera/Brettanomyces. After the fermentation is finished, the beer is cleared of the yeasts by precipitation or with the use of clearing additives.

Other types of alcohol beverages are made by the fermentation activity of microorganisms as well. A few examples are sake (uses the fungus Aspergillus oryzae to facilitate starch fermentation from rice), brandy, whiskey (both are distilled alcohol), and other alcohol beverages with higher percentage of alcohol compared to wine and beer.

Vinegar

Vinegar is a food product made by acetic acid bacteria that can ferment the alcohol in alcoholic liquids to acetic acid.

At the domestic level……

The foods that are prepared by keeping overnight; basically exploit the functions of the general microbes in the air who feed on the food and the nutrient present in it.

The preparation of Dosai,Idlly, Hoppers involve this process, and your grandma will know about this better than anyone! She would just look at the extent of the dough-rise and tell you whether it is ready for food preparation or not.

Image courtesy : 

https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcSf8vph3BnMnthQrPIFgdUuX789RKka3vzef3_0kD0X6ZpqFozNfw&s

http://bit.ly/30C4SAf

https://image.shutterstock.com/image-illustration/set-cartoon-monsters-funny-smiling-260nw-655094149.jpg

https://static.toiimg.com/photo/70409111.cms

https://static.vinepair.com/wp-content/uploads/2019/10/HopTake-Oct17-Header.jpg

https://www.grocerypal.lk/media/catalog/product/cache/1/image/800×552/9df78eab33525d08d6e5fb8d27136e95/h/i/highland_yogurt.jpg

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Name:R.Vinushayini

INdex : s13350

Usually foods are material that origin from any plant or animal. That contain essential body nutrients. Such as carbohydrates, fats, proteins, vitamins or minerals. All food should be safe and free from contamination and spoilage at all points in its journey from its source until it reaches the consumers.

However food contamination is a serious public health problem in global. Resulting in foodborne disease that affect many people every year. Hence, awareness of potential sources of food contamination is an important component of good nutrition and good health. In this article we are going to concentrate on food contamination by microorganism, chemicals and physical factors that cause to spoilage, foodborne diseases and preservation.

Food may be contaminated by different microorganisms or by chemicals that can cause health problems for anyone who eats it.Therefore we need knowledge to identify whether it spoiled or not? Food spoilage is the process of change in the physical and chemical properties of the food so that it becomes unfit for consumption. Most natural foods have a limited life: for example, fish, meat, milk and bread are perishable foods, which means they have a short storage life and they easily spoil. Other foods also decompose eventually, even though they keep for a considerably longer time. The main cause of food spoilage is invasion by microorganisms such as fungi and bacteria. Change in nutrition value, change in organoleptic features and unwholesome effects can be used to identify spoilage foods. 

In spoiled foods, mainly change their organoleptic features. Organoleptic features are the aspects of food, water or other substances that create an individual experience via the senses including color, flavour, taste, smell, appearance and consistency. Therefore one or several features can be changed under unfavorable condition. Mucilaginous surface is the best example for appearance changes. Having Bad odour and sour are the some indication that it may be unsafe. For an example: When food is covered with a furry growth and becomes soft and smells bad, the spoilage is caused by the growth of moulds and yeasts. Microbial spoilage by moulds and yeasts includes souring of milk, growth of mould on bread and rotting of fruit and vegetables. These organisms are rarely harmful to humans, but bacterial contamination is often more dangerous because the food does not always look bad, even if it is severely infected.

 Unwholesome effects also can be happen because of their biogenic amines, toxins, metabolites of microorganism and pathogenic organism. 

Nutritional value can be changed by decomposition of proteins, carbohydrates and vitamins. Under this one nutrient can be converted in to toxic materials. When microorganisms get access to food, they utilize the nutrients found in it and their numbers rapidly increase. Growth of microbes in food follows a typical microbial growth pattern.it depends on the nutritional value and temperature of the food. Food spoilage is noted at a particular population density. 

The growth of microorganisms in food products can be affected by extrinsic factors and intrinsic factors. By understanding the factors affecting the growth of microorganism in food we can know how to keep food safe to eat. It will help to preserve food for long time.

Extrinsic factors are factors in environment. That factors external to the food. Extrinsic factors include temperature, humidity, atmosphere composition, processing effects, hygiene, cleaning and disinfections.       

Different microorganisms grow over a wide range of temperatures. Some microorganisms like to grow in the cold, some like to grow at room temperature and others like to grow at high temperatures. If you know the temperature growth ranges for dangerous microorganisms it helps you to select the proper temperature for food storage to make them less able to grow and reproduce. Optimum temperature between 10⁰C to 80⁰C.Under the minimum temperature growth will stop and above the maximum temperature microbes are killed.

The humidity of the storage environment is an important factor for the growth of microorganisms at the food surfaces. If you store food in a dry atmosphere, microorganisms are less able to grow than if the food is stored in a moist environment. Therefore, dry conditions are better for food storage than moist condition.

 Many microorganisms need oxygen in order to develop and reproduce. These are called aerobic microorganisms. Example: Escherichia coli – a faecal bacterium which grows readily on many foods.

 If you keep food in a low oxygen environment, aerobic bacteria cannot grow and multiply. Conversely, there are some microorganisms that grow without oxygen, called anaerobic microorganisms. Example: Clostridium botulinum, the bacterium causing botulism, which can survive in very low oxygen environments such as tinned foods.

Intrinsic factors that are characteristic to the food. Physical-Chemical properties, chemical composition and biological structure are main category under intrinsic factors. Physical – Chemical properties including water activity (a_w), redox circumstances and pH. Nutrient materials, vitamins, inhibitors are including under chemical composition.

Microorganisms need a moist environment to grow in. The water requirements of microorganisms are described in terms of water activity (a_w).A measurement of how much water is present. The water activity of pure water is a_W = 1.00. Most foodborne pathogenic bacteria require a_W to be greater than 0.9 for growth and multiplication. However, Staphylococcus aureus may grow with a_W as low as 0.86.If we want to ensure the safe storage life the a_w has to be reduced under 0.7.

 Most microorganisms grow best at close to the neutral pH value (pH 6.6 to 7.5). Only a few microorganisms grow in very acid conditions below a pH of 4.0. Bacteria grow at a fairly specific pH for each species, but fungi grow over a wider range of pH values.

 For example, most meats naturally have a pH of about 5.6 or above. At this pH meat is susceptible to spoilage by bacteria, moulds and yeasts; however the pH of meat can be lowered by pickling, which makes it less favourable as an environment for microorganisms to grow in.

                                       

Redox potential depends on the concentration of oxidizing and reducing agents. That mean amount of Oxygen that present in the food material will determine whether it is aerobic or not. Redox potential requirement for microorganisms are shown below.

    Aerobic microbes: > 300mV

    Anaerobic microbes: < 300mV

Under composition of foods contain nutrient content and structure of food items. In order to grow, multiply and function normally, microorganisms require a range of nutrients such as nitrogen, vitamins and minerals. Microorganisms therefore grow well on nutrient-rich foods.

The natural covering of some foods provides excellent protection against the entry and subsequent damage by spoilage organisms. Examples of such protective structures are the skin of fruits and vegetables such as tomatoes and bananas.

Food can be contaminated from sources in the natural environment, people, food preparation surfaces and utensils, raw and uncooked food, animals, pests, and waste material. Spoilage, foodborne illnesses, toxin production and bring about unfavourable changes are resulting microbial activity on food. Foodborne illnesses is any illness resulting from the spoilage of contamination food, pathogenic bacteria, viruses that contaminated food as well as toxins. It can be mainly in two category. Food borne infection happen due to ingestion of active microbes containing food. And food poisoning happen due to ingestion of toxins. Ergotism is the one of the illnesses that result from fungus toxin. Aflatoxins and Fumonisins are other toxin compound that produced by fungus. Most are infections and associated with animal products.

Therefore food production and preparation operations need to be carefully controlled to prevent contamination. Prevention of microbiological contamination is an important function in food preparation. Therefore need to follow preservation technique to minimize the massive losses of foods.

Food preservation is a technique that can be used to prevent or remove of contaminate. Such a preservation technique inhibit the growth and metabolic activity of microorganism. It renders the food being a bad medium for growth. Killing or sterilization technique destroy the number of microorganism initially present on or in the food .Finally it prevention of recontamination. Food preservation technique are aseptic handling, temperature, lowering a_w, chemicals and radiation.

Temperature is the one of the safest and most reliable technique. At high temperature destroy organisms in canned and bottled food. When temperature become high enzyme inactivation occur. Because of the protein denaturation .Then it helps to prevent autolysis. However some food cannot be heat treated. It affect the color, texture and nutrition value also. Milk is the best example. At low temperature, slow down the enzymatic action and delay autolysis. In household fridge 5⁰C prevent growth of many spoilage organisms.

Reducing water activity (a_w) is another preservation technique. Growing of microbes can be inhibited by maintaining a critical a_w. This critical value is determined by the characteristics of the particular organism and the capacity of the food to bind water. So that It is not available as free water. After drying, store in a cool dry place. For an example: Fresh fruits contain 25-30% of sugar and acid and milk contain 2%of the original moisture. Water availability can be reduced by using sun-drying, spray drying, freeze drying and evaporation.

Chemical –based preservation can be done by using chemical agents that are legally accepted. Benzoic, sorbic, proponic, lactic and acetic mainly used organic acid. Sorbic and proponic acid inhibit the growth of mould. Many of the chemical compound are safe to human. Some may affect human health also. For an example: nitrites used as chemical preservation compound in meat production. However it harmfully effect the human health. Because it is a carcinogenic compounds.

Radiation is another preservation technique widely used in developed country. Ultraviolet (UV) radiation and ionizing radiation are mainly used. UV radiation is powerful bactericidal radiation used for surfaces of food –handling equipment. Does not penetrate foods and sterilize cold storage rooms. Ionizing radiation used to extend shelf life or sterilize meat, seafood, fruits and vegetables. Radiation dependent on dosage. Sometime high dosage infect on human health also. Finally products need to be labeled as irradiated. 

By using proper technique, we can preserve the food from microorganisms. Canned food is best example for it. Therefore one of the main, and most effective, ways of protecting food consumers is to prevent food from becoming contaminated by pathogenic microorganisms.

Image credits:

Figure 1 : https://www.bbc.com/future/article/20170224-what-food-would-keep-you-alive-the-longest

Figure 2 : https://www.alamy.com/stock-photo/hyphae.html?cutout=1

Figure 3 : https://www.123rf.com/photo_60637725_old-white-mold-on-bread-spoiled-food-mold-on-food-.html

Figure 4: https://www.istockphoto.com/video/spoiled-food-gm697162782-130131521

Figure 5:https://www.foodonline.com/doc/ensuring-food-safety-through-the-prevention-of-physical-contamination-0001

Featured Image: https://www.sciencesource.com/Doc/TR1_WATERMARKED/6/1/b/0/SS2116540.jpg?d63641180462

–
Achani Madhushani

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You may have heard that human body is inhabited by trillions of microbes such as bacteria, viruses and fungi, but did you know that the number of microorganisms in your body is more than the number of cells of your body? Yes, your body is a home for trillions of microbes and these microbial communities are totally known as human microbiome. In science, human microbiome is considered as a virtual organ which is very important and essential for host survival. Although human microbiome is not same or identical for two individuals it can be very similar. Human microbiome is considered as a source of genetic diversity. However, microbiome of the same person can be changed due to the food he eats, the medicines he takes and the environment he lives etc. These microbes inhabit in various parts of the body including both external and internal organs where they have adapted to live in. Microbes are predominantly found in skin, oral cavity, nasal cavity, digestive gut and vagina etc. The microbial communities that are found in and around various body parts are different to each other. Usually humans are born sterile and we acquire our own microbiome during the birth process and immediately after birth. After that when we grow with time, we are exposed to different kinds of microbes in various ways due to the different interactions that we make with the environment and living beings. During this growing period microbes that are associated with our body can be changed and it will be more or less stable after around 3 years old. The person’s age, sex, mode of delivery, diet, genetics, cleanliness and the environment he lives make impacts on the establishment of the microbiome. 

These tiny living organisms live with us throughout our life involving in healthy growth, in aiding proper digestion, in protecting body. Generally, humans have a balanced microbiome which can be interrupted by the food style, excessive use of antibiotics, lack of personal hygiene practices, variable host immune response and fluctuating environmental conditions. The interaction between human body and microbes is important for both groups to grow and stay healthy.  Commensalism and mutualism are the types of relationships that are seen between these two groups. Thus some microbes co-exist in or on the human body without causing any harm representing commensal relationship and mutualism is shown in some interactions since it is beneficial for both groups. Most of the times the microorganisms that are associated with human body do not cause any harmful effects except for certain conditions. However, sometimes these microorganisms can grow beyond the typical numbers or colonize in areas where considered to be sterile and they are usually not growing. In such cases microbes are considered as pathogenic and will result diseases. For example, if blood contains microbes due to a compromised immune system, it is considered as a disease called bacteremia. Sometimes pathogens that remain dormant earlier in the human body can be infectious resulting diseases if favorable conditions occur.

Various types of microbes are living in and on the human body such as bacteria, viruses and fungi. Various species of microbes are found in different parts of the body depending on the conditions of the location and the species that live there have adapted to those conditions. Therefore, the same species may not be found in different parts of the body. Actinomyces are found in the oral cavity as a part of a sticky substance called plaque, representing group of bacteria. Lactobacillus species are also group of bacteria that are mostly found in vagina. Fungi are also present in and on the human body and in particular they are Yeast. Candida albicans is the most prominent species that are found in the human body. It is mostly found in the gut and sometimes in mouth also. Oils secreted from the sebaceous glands are consumed by Malassezia species that are living on the skin. 

When considering the diversity of microbes living in the human body, most diverse population lives in the skin since the skin is the largest organ of the human body. Among the different kinds of microbes that live on the skin bacteria population is higher than fungi and viruses. Usually these microorganisms are found in the upper parts of the epidermis and some are colonized in and around the hair follicles. Most of these microorganisms are harmless and there may be beneficial groups also. Skin and the microorganisms together act as a physical barrier and protect our body from the invasion of pathogenic or harmful microbes which can enter to the body to cause diseases.  For instance, Bacillus subtilis which is found on skin produce bacitracin, a toxic compound that helps to fight against the establishment of harmful microbes on the skin. In the dry zones of the skin such as hand, legs and feet most diverse microbe population is resident because those sites are very much exposed to external environment. Not only in the dry areas, but also in moist areas such as elbow creases, in-between toes and beneath the breasts and the oily areas where sebaceous glands are present also provide residence for the microbiome. Any fold on the skin such as under arms, breast fold and groin area and navel usually have a high number of microbes. After the initial colonization of microbes on the skin of a newborn baby various factors affect microbial growth on the skin. Moisture, temperature, skin pH, sun exposure and even the genetic makeup of the individual influence the skin microbiome. Common genera that are found on the skin are Staphylococcus, Micrococcus, Corynebacterium and Malasezzia. 

Gut is the place where the most number of microorganisms are found among the microbial residences of the human body. It is said that 70% of the microbiome consists of gut microbiome. These microbiota helps to protect the gut wall from pathogens while some are facilitating the digestion process. There are some microorganisms in the gut that produce vitamin K and vitamin B12 which are not able to produce by human cells. Recent studies show that gut bacteria can affect your appetite as well in addition to the use of energy from food. Certain microbes produce enzymes and/or chemical compounds to prevent colonization of pathogenic microorganisms. The gut microbiome of infants is distinct from each other based on their mode of delivery and the feeding habits. However, the gut microflora of each infant becomes distinct at the end of the first year of life and within maximum three years it is fully resembled in terms of adult microbiome. The present groups of microbes usually change from place to place through the digestive tract and also from a healthy person to diseased person. Any change in gut microbiota can lead to several metabolic diseases and changes based on age, weight, nutrition and diet, life style, genetic variation etc. 

Oral microbiota is another important part of the human microbiome and also one of the most complex microbial communities. Microorganisms in the oral cavity enter the digestive tract through saliva. Unlike the gut, diet and the environment have only a minimal impact on the oral microbiome. Bacteria is the dominant group of microbes that are present in the oral cavity over fungi and other groups. Candida species are found in mouth representing fungi. They act normal in the balanced oral microbiota and can attack oral tissues when the balance is broken down.

Nasal cavity is another place where microorganisms are colonized. There are different types of microbes in the different locations of the nasal cavity. Streptococcus, Staphylococcus, Corynebacterium are some of the main types that are found in nasal cavity. Nasal cavity microbiome is also acquired by humans in the first year after birth and it has fluctuations throughout the life. The composition of nasal cavity microbiome may have impacts on the lower respiratory tract and other invasive infections.

Microbes that live in the vagina are beneficial to humans as they maintain an acidic environment in the vagina. This acidic environment prevents the colonization of any other harmful microorganisms. Therefore, any disturbance to the vaginal microbiota can be infectious. Vaginal microbiota feed on secretions from vaginal mucosa. Lactobacillus genus is dominant in vagina and few species of the genus Lactobacillus can occur. They maintain acidic pH by producing lactic acid. Additionally, competitive exclusion and the production of bacteriostatic and bactericidal by Lactobacillus are also important. When the population of other microbe groups such as fungi or bacteria rise over the dominating group Lactobacillus, infections can occur. pH increase in the vagina also can cause infections in some situations. Presence of healthy microflora in the vagina leads to successful reproduction while preventing possible diseases such as yeast infections, bacterial vaginosis, urinary tract infections and even sexually transmitted diseases.

As mentioned earlier, microbes can be harmful to humans when pathogenic microbes enter the human body disrupting the normal microbiome. There are few possible sites that microbes can enter the human body. They are gastrointestinal tract, respiratory tract, urogenital tract and injured skin. Even though they enter the body there are some other steps to be completed to make a disease. First they should reach and attach the target site of the body and then they should multiply there rapidly. With the colonization microbes obtain nutrients from the host and they will survive by avoiding the attacks from the immune system. Pathogenic microorganisms are transmitted to human body mainly from another person, from water or from food. Pathogenic microbes can transmit from person to person by touching, contaminated blood, saliva or air. Food and water are also routes of transmission for microbes. Although antibiotics are taken as treatments for a particular disease, normal microbiome can be disrupted by excessive use of antibiotics. Since antibiotics kill microorganisms, beneficial microorganisms also can be affected and it will create a favourable environment for pathogenic microbes to grow. Thus it is necessary to maintain right combination of microbes and immune system to stay healthy. 

However, a balanced and diverse microbiome is essential for the survival of the human body as it has a key role associated with the immune system. Therefore, it is important to take care of our own microbiome considering it as part of the body to make our body functioning properly. 

Image courtesy 

Figure 1- https://link.springer.com/chapter/10.1007/978-981-10-7684-8_1

Figure 2- https://www.alamy.com/computer-illustration-of-the-human-digestive-system-and-bacteria-found-in-it-some-bacteria-such-as-lactobacillus-and-bifidobacterium-have-beneficial-functions-and-are-part-of-normal-microbiota-others-such-as-helicobacter-pylori-and-salmonella-cause-disease-image189002868.html

Figure 3- https://www.google.com/imgres?imgurl=https%3A%2F%2Fimage.slidesharecdn.com%2Fvirulence-120407074245-phpapp01%2F95%2Fbacterial-virulence-4-728.jpg%3Fcb%3D1333786480&imgrefurl=https%3A%2F%2Fwww.slideshare.net%2FMansManchester%2Fvirulence-12307872&tbnid=pDLq6I3ITn-MbM&vet=12ahUKEwi08ODG7YrnAhVHxHMBHSubBm4QMyhOegUIARCrAQ..i&docid=8tLIbnk71Q6XiM&w=728&h=546&q=pathogenic%20microbes%20in%20humans&hl=en&ved=2ahUKEwi08ODG7YrnAhVHxHMBHSubBm4QMyhOegUIARCrAQ

References 

Anon, (2017). [ebook] Available at: https://www.longdom.org/open-access/role-of-microbes-in-human-health-2471-9315-1000131.pdf [Accessed 5 Jan. 2020].

Saluni Chaneesha

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           In forest soils, their chemical fertility is generally limited.And forest soils are very acidic and organic.These forest soils are heterogeneous in nature.Their characteristics changes with mountainous,environment and altitude.The forest soil is acidic with low humus content in the snow covered area.The soil is loamy with slity in vally side and coarse grained in the upper slopes.

        The biological characters of the soil include the population of plants and animals including microflora (Fungi,Bacteria,Algae)and microfauna (worms,arthropods,protozoa).Forest microorganism perform many complex tasks relating to soil formation ,slash and litter disposal,nutrient availability and recycling,and tree metabolism and growth.Generally the number of organisms are greatest in the forest floor and the area directly associated with plant roots.

        The population of soil organisms(both density and composition)and how well that population thrives is dependent on many soil factors including moisture,aeration ,temperature,organic matter,acidity and nutrient supply.(Pritchett 1979)

         The two groups exerting the greatest influence on soil processes are the nematodes and protozoa.

Nematodes

          They are commonly called threadworms or eelworms found in almost all soils,often in surprisingly large numbers.They are unsegmented round worms 4 to 100 µm in cross sections and up to several millimeters in length.This is a highly diverse group.Most nematodes are predatory on other nematodes ,fungi,bacteria,algae,protozoa,and insect larvae.Some nematodes specially those of the genus Heterodera,can infest the all plant species by piercing the plant cells with a sharp spearlike mouth part.These wounds often allow infection by secondary pathogens and cause the formation of knotlike growths on the roots.

Protozoa

          Protozoa are mobile,single celled creatures that capture and engulf theirfood.They are the most varied and numerous of the soil microfauna.More than 350 species of protozoa have been isolated in soils;sometimes as many as 40 to 50 of such groups occur in a single sample of soil.The liveweight of protozoa in surface soil ranges from 20 to 200kg /ha.

       Protozoa generally thrive best in moist,well drained soils and are most numerous in surface horizons.Protozoa are specially active in the area immediately around plant roots.Their amin influence on organic matter decay and nutrient release is through their effects on bacterial populations.

Soil Algae

          Most soil algae range in size from 2 to 20 µm.Many algal species are motile and swim about in soil pore water,some by means of flagella.Most grow best under moist to wet conditions , but some are also very important in hot or cold dessert environments.Sometimes the growth of algae may be so great that the soil surface is covered with a green or orange algal mat.Some algae form lichens ,symbiotic associations with fungi.These are important in colonizing bare rock and other low –organic –matter environments.Unvegetated patvhes in desserts commonly are covered with algal crusts that reduce water evaporation and soil erosion but are very sensitive to distruption by trampling or off-road vehicles.

        Although there are several thousand species of algae in soil small number of species are most prominent in soils throughout the world.Soil algae can be divided into three general groups.

(1)Green algae-most evident in moist but nonflooded scidic soils

(2)Yellow-green

(3)diatoms-often numerous in neutral to alkaline

    Algal populations commonly range from 1 to 10 billion per square meter,15-cm deep.(10,000 to 100,000 cells per gram)

Soil Fungi

        Soil fungi consists of extremely diverse group of microorganisms.Tens of thousands of species have been identified in soils representing some 170 genera.As many as 2500 species have been reported in a single location.Scientists believe there are at least 1 million fungal species in the soil still awaiting disccovery.Their biomass in soils commonly ranges from 1000 to 15,000 kg/ha in the upper 15cm.Fungi can be divided as yeast,molds and mushrooms.

Molds

      These are significantly filamentous,microscopic or semimacroscopic fungi that play a much more important role in soil organic matter breakdown than the mushroom fungi.Molds develop vigorously in acid,neutral or alkaline soils.The ability of molds to tolerate low pH is especially important in decomposing the organic residues in acid forest soils.Four of the most common are Penicillium,Mucor,Fusarium and Aspergillus.

Mushroom Fungi

      These fungi are associated with forest and grass vegetation where moisture and organic residues are ample.The aboveground body of most mushrooms is only small part of the total organism.An extensive network of hyphae permeate the underlying soil or organic residue.While mushrooms are not widely distributed as the molds,these fungi are very important ,especially in the breakdown of woody tissue,and because some species form a symbiotic relationship with plant roots.

     As decomposers of organic materials in soil  ,fungi are the most versatile and persistent of any group.Cellulose,starch,succumb to their attack.Fungi play major roles in the processes of humus formation and aggregate stabilization.They usually dominate in the upper horizons of forested soils,as well as in very acid or sandy soils.

Soil Actinomycetes

           Aerobic heterotrophs,they live on decaying organic matter in the soil,or on compounds supplied by plants with which certain species from parasitic or symbiotic relationships.Many actinomycete species produce antibiotic compounds that kill other microorganisms,In forest ecosystems,much of the nitrogen supply depends on certain actinomycetes that are capable of fixing atmospheric nitrogen gas into ammonium nitrogen that is then available to higher plants.

        Actenomycete number in soil exceed those of all other organisms except bacteriaWith their biomass as high as 5000 kg/ha,they often exceed the bacteria in actual liveweight.The earthy aroma of organic rich soil and freshly plowed land is mainly due to actinimycetes products called geosmins that are volatile derivatives of terpene.

Soil Bacteria

       The number of bacteria are extremely variable,but high,ranging from a few billion to more than a trillion in each gram of soil.A biomass of 400 to 5000 kg/ha liveweight is commonly found in upper 15 cm of fertile soils.

       Their extremely rapid reproductive potential enables bacteria to increase their populations quickly in response to favorable changes in soil environment and food availability.Soil bacteria are either autotrophic or heterotrophic.Heterotrophic bacteria often predominate on easily decomposed substrates,such as animal manures,starches and proteins.Bacteris as a group posses such a broad range of enzymatic capabilities,scientists are now finding ways to harnessing,even improving,the metabolic bacteria to help with the remediation of soils polluted by cruid oil,pesticides,and various other organic toxins.

References

https://www.sciencedirect.com/topics/earth-and-planetary-sciences/forest-soil

https://.wiley.com/doi/abs/10.1002/9781119438069.ch7

http://nwdistrict.ifas.ufl.edu/phag/files/2018/11/Southern-root-knot-nematode-Meloidogyne-incognita-Scott-Bauer-USDA-Agricultural-Research-Service-Bugwood.org-1323037.jpg

Image courtesy

http://nwdistrict.ifas.ufl.edu/phag/files/2018/11/Southern-root-knot-nematode-Meloidogyne-incognita-Scott-Bauer-USDA-Agricultural-Research-Service-Bugwood.org-1323037-207×300.jpg

http://nwdistrict.ifas.ufl.edu/phag/files/2018/11/nematode-Steinernema-scapterisci-entomopathogen-of-scarab-larvae.-Stage-is-infective-juvenile.-entomopathogen-of-scarab-larvae.-Stage-is-infective-juvenile.-5351012.jpg

https://ars.els-cdn.com/content/image/1-s2.0-S0167880999000328-gr1v9.jpg

https://www.algalweb.net/SHEW/Sept12/Botrydium-1.jpg

http://cdn.shopify.com/s/files/1/0150/6262/articles/mushrooms_and_fungi_1024x1024.jpg?v=1529080232

https://media.sciencephoto.com/image/c0322284/800wm

https://c8.alamy.com/comppt/egebe1/podridao-tronco-de-arvore-em-decomposicao-no-solo-da-floresta-egebe1.jpg

Nimesha Sewwandi

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Bioremediation of polluted water by using micro-organisms

Water pollution, one of the popular topic talking from decades to decades. But still has no permanent solution.

Water pollution occurs due to the leakage of pollutants or by the direct discharge of the pollutants to the water resources. However, the contamination of these water bodies leads to a decrease the amount of usable water. So due to the growing population, water demand is increasing. 

Contamination of solid waste can be removed by the water treatment plants, but contamination of particulate matter cannot be easily removed. Contamination of heavy metals, organic waste, oils, and pesticides are major problems which have a great concern in the world.

Thus with the growing knowledge of science, people have found an efficient method for water pollution. Bioremediation, the word might not familiar yet for everyone. 

Bioremediation is a process that uses naturally occurring or introduced micro-organisms for the cleaning of polluted sites by converting toxic substances to non-toxic substances. So by using various kinds of microorganisms, polluted water can be recovered for a limit that is not harmful to the environment.

For this process micro-organisms with different biological activities such as algae, bacteria, fungi, and yeast. When introducing micro-organisms for the bioremediation process, they should be carefully selected because the survival of the micro-organisms should be ensured in the polluted site. The maximum capacity of the survival and the efficiency of the process should be considered.

Bioremediation strategies

• In-situ remediation

In in-situ remediation, the bioremediation process conducted in the contaminated site. Contaminants are not removed. Most desirable strategy due to the cost efficiency, minimal disturb to the environment and avoiding the transport of the contaminants.

• Ex-situ remediation

in ex-situ remediation, bioremediation is done not in the contaminated site. Pollutants/ contaminants removed and treated somewhere else and returned back to the site.

Factors affect to bioremediation

Environmental factors	Pollutant characteristics	Microflora activity
pH	Solubility of pollutant	Biomass concentration
Temperature	concentration	Population density
Oxygen and other      molecules present	Bio availability	Enzyme activities
Nutrient availability	Ability to serve as carbon source
moisture
Osmotic potential

Table 01: factors affecting to the bioremediation

Environmental factors 

There are few critical environmental factors that affect to the bioremediation process

• pH

The pH of the contaminant directly affecting the microbial growth because the by-products acids produce in the degradation process. Therefore the ph reduced and many bacteria and algae can not grow in those sites. Best range from 6.50 to 7.5 

• Temperature 

Temperature is also affecting the growth of microbes. It directly affects to the enzyme activity and the metabolism of the microbes. Not preferably grow in the freezing conditions.

• Oxygen and other molecules

The presence of Oxygen and other molecules that can act as the terminal electron acceptor are more important for their respiration.

• moisture

Moisture or the relative humidity is considerable should be in higher amount but in water remediation, it is not a critical factor. 

 Presence of the Nutrients like nitrogen, phosphorus, sulfur and other nutrients supports the growth of the microorganism 

• Osmatic potential/concentration of the pollutant

If the pollution concentration is higher in the water then the osmatic potential of the water is less. Then the available water for the microorganism is less.

Pollutant characteristics

• The solubility of the pollutant

If the solubility of the contaminant is higher, it is easier to degrade the contaminant.

• Ability to serve as a carbon source.

In the bioremediation process, the contaminant or the pollutant act as the substrate or a carbonic source to the microorganisms. Therefore if the substrate is more effective to act as a carbon source the bioremediation is more effective. 

Micro flora activity

• Population density

Population density of the microorganisms is another major factor affects the efficiency of the bioremediation process. If the population density is higher, effective of the process is also higher.

• Enzyme activity

Enzyme activity of the micro flora is totally depending on the environmental factors as well as the species of microorganisms. 

How the bioremediation applied to remove the contaminants.

• Heavy metal accumulation

Heavy metal accumulation of the water bodies is a serious problem that threatens both humans and environment. Accumulation of heavy metals like leads to disrupt the food chains by accumulating in higher. some of these metals are essential micronutrients in organisms, hence high absorption of these metals in higher concentrations is toxic to them. Therefore the biological activities are not functioning well in these organisms.

To overcome this issue bioremediation can be used. Following organisms are widely used for the process, bacteria: Arthrobacter spp., Pseudomonas veronii, Burkholderia spp., Kocuria flava , Bacillus cereus, and Sporosarcina ginsengisoli; fungi: Penicillium canescens , Aspergillus versicolor, and Aspergillus fumigatus; algae: Cladophora fascicularis, Spirogyra spp. and Cladophora spp., and Spirogyra spp. and Spirullina spp.; and yeast: Saccharomyces cerevisiae and Candida utilis.

• Oli spillages 

Oil spills in the ocean or the other water bodies highly affected the aquatic animals and plants. the birds living in those aquatic ecosystems are also affecting since there are regularly feeding on the fish. organisms like filter feeders also highly affected by oil spills.

Most of the organisms can utilize oil as there food source, by using these organisms oil spillages can be cleaned. Bacteria that can degrade petroleum products include species of Pseudomonas, Aeromonas, Moraxella, Beijerinckia, Flavobacteria, Chrobacteria, Nocardia, Corynebacteria, Modococci, Streptomyces, Bacilli, Arthrobacter, Aeromonas, and cyanobacteria and some yeasts. For example, Pseudomonas putida. These organisms increase the rate of oil degradation due to the high potential capacity of remediation.

• Remediation of the organic contaminations

Most of the organic waste is dumping by the industries to the water bodies directly. Microbes have the potential to degrade the organic compounds and produce non-toxic compounds like carbon dioxide(CO₂), water and minerals.

• Remediation of the pesticides

Leakage of the pesticides to the water is another major problem regarding the agriculture industry. As earlier mentioned the microbes which have the potential to degrade organic materials can be used for this remediation. those organisms are using these pollutants as their food source and degrade by using their enzymes. 

• Remediation of the Eutrophication

Eutrophication is another environmental problem that occurs due to the accumulation of nutrients in the water bodies. The leakage of the fertilizers and the fecal matter from the farms is leading to increase the concentration of the nitrogen and phosphorus concentration. Therefore algal growth gets increase and reduces the available light intensity, nutrients, and oxygen for the other aquatic organisms. At the end of this process, the aquatic ecosystem destroyed. 

Microbes can use to overcome the eutrophication. By using several microorganisms the concentration of the main causing nutrients like nitrogen and phosphorus can be reduced.

Applications of bioremediation

Bioremediation is applied to certain sites that have considerable potential to pollute the environment by leaching the materials the used.

These are a few examples, where bioremediation is widely used.

• Petroleum stations 

Usually, petroleum stations have established underground tanks. Poor maintenance of those tanks, damages and when remaining long after the station’s service life expired. Can leach gasoline and diesel fuel into the water reservoirs. Bioremediation is applied to those areas to minimize the effects of contaminations. 

• Industrial sites 

Chemicals used for the various productions and the by-products are spilled or discharged in the effluent into the water bodies. Some contain heavy metals like lead and chromium. Those contaminants are tough to remediate.

• Landfills

Landfilling has been practiced as a solution for land pollution, thus overfill or leach can be caused to pollute the groundwater resources. Bioremediation is well suited to minimize the effects arise from landfilling.

• Farms 

Agricultural farms where over-application of fertilizers and pesticides occurred and farms where animal waste products are leached can use bioremediation to overcome the issues. This protects the groundwater bodies as well as the surface water bodies.

• Lumber processing yards

often polluted from wood preservatives. They commonly leach into the soil and groundwater but can be cleaned up through bioremediation,

Benefits of the bioremediation

• Bioremediation is a Natural Process

Bioremediation has won public acceptance to a certain extent since it is a biological process. Through this process, no harmful products are generated and degrade the contaminant pollutants in the water bodies (applicable for soil).

• Complete Destruction

Through the bioremediation process, the complete destruction of hazardous wastes and other contaminants can be done. Therefore many pollutants have transformed into less harmful products.

• On-Site Treatment

The bioremediation process can be carried out at the site where the contamination occurred. Therefore no need to transport and thus minimize the effects of the contamination as well as the distribution of the contaminants.

• Cost-effective

Since it is a biological process use of types of equipment and chemicals is minimum. And most of the contaminated sites are treated and on-site treatment. Therefore less energy is consumed.

• High acceptance from the authorities 

Due to the minimum effects of the procedure and the feasibility of the process, most of the countries are tend to practice the bioremediation treatment.

• Easy to conduct

The process also does not require any additional land or power, making it a simple and easy system.

It is cheaper than conventional treatment methods, easy to handle and, importantly, does not require skilled manpower.

Limitation of Bioremediation

• Specificity

Bioremediation is a highly specific biological process. Since it associates with the use of microorganisms many factors that affect them should be considered. Microorganisms are using the contaminant as the substrate to produce energy. Therefore particular microorganisms that can degrade the pollutants should choose for the treatment. On the other hand, the growth of the microorganisms should facilitate initially by providing fertilizers and oxygen to the contaminant sites. Also before the treatment should ensure that the substrate (contaminant) is not toxic or the by-products generated from the treatment is not toxic to the environment.

• Technological Advancement

More research and developments should be done regarding the improvement of the treatment and the application of bioremediation is less in developing countries. 

• Time Taking Process

Compared to the treatments using chemicals for the degradation of pollutants, it is a more time-consuming process. For considerable efficiency, there should be an optimum amount of population density.

• Regulatory Uncertainty

In this process, the endpoint of the process can not be given as all the contaminants are removed. Therefore accepted or defined evaluation should be introduced.

• Depending on the strategy

In situ strategy takes more time compared to the ex-situ strategy. In situ strategy is more effective in the permeable soils (sandy soil).

• Habitat 

More effective in the mesophilic or thermophilic habitats, since the enzyme activity needs considerable higher temperatures, remediation can not be done in the sites which have freezing temperatures.

Bioremediation to Sri Lanka

Internationally several countries are using bioremediation technology. In Sri Lanka still, water pollution has not become a considerable environmental problem. Also, there are none of drastically contaminations happened to the water resources. Thus the current status of the wastewater treatments would not be enough to treat the wastewater in the future. 

Bioremediation is a cost-effective technology, as mentioned earlier it is more efficient to practice in situ and time-consuming.  Hence if bioremediation introduce in this era it would be more effective in the sustainable management of water. 

Currently, some of the lakes in urban areas are highly contaminated with pollutants. Even it can not use for the drinking purposes it can be clean to a certain extent that helps to reduce the bad odor, spreading of diseases

Today in Sri Lanka number of the patients that have kidney diseases is getting increasing and still, a permanent solution has not been discovered. And still, some rural and urban areas do not have proper sanitation facilities and all of the wastewater is discharged into the nearby water body.  With the increasing of the population a proper way of treating wastewater efficiently, should be found.

Therefore the establishment of modern technology like bioremediation would be more effective and beneficial for the future of the developing country like Sri Lanka.

Image courtesy

http://www.mebotek.be/products/bioremediation-products/bioremediation-before-after/

https://images.livemint.com/r/LiveMint/WebArchive/BP/Photos/2015-07-21/Processed/Mint/Web/w_g_Science_Bioremediation.jpg?_ga=2.245211653.1280130806.1580989402-18125137.1578119240

https://www.intechopen.com/books/advances-in-bioremediation-of-wastewater-and-polluted-soil/bioremediation-of-polluted-waters-using-microorganisms

https://www.svcf.ru/en/env/services/oil-spills-readiness.html

https://static.wixstatic.com/media/f7f0c0_b22121f4070547248e0f71d12823467a~mv2_d_1800_1200_s_2.jpg

Sandali Nimnika Sarathchandra 

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The first antibiotic that didn’t work for Debbi Forsythe was trimethoprim (antibiotic #1). In March 2016, Forsythe, a friendly primary care counsellor from Northumberland, England, contracted a urinary tract infection (UTI). UTIs are common: more than 150 million people worldwide contract one every year. So when Forsythe saw her GP, she was prescribed the usual treatment: a three-day course of antibiotics. When, a few weeks later, she fainted and started passing blood, she saw her GP again, who again prescribed trimethoprim (antibiotic #1).

Three days after that, Forsythe’s husband Pete came home to find his wife lying on the sofa, shaking, unable to call for help. He rushed her to the hospital. She was put on a second antibiotic, gentamicin, and treated for sepsis. The gentamicin (antibiotic #2) didn’t work either. Doctors sent Forsythe’s blood for testing, and five days after she was admitted to hospital, Forsythe was diagnosed with an infection of multi-drug-resistant E coli.

Antibiotics – The Superheroes 

Before scientists first discovered antibiotics in the 1920s, many people died from minor bacterial infections, like strep throat. Surgery was riskier, too. The introduction of antibiotics into medicine revolutionized the way infectious diseases were treated. After antibiotics became available in the 1940s, life expectancy increased, surgeries got safer, and people could survive what used to be deadly infections. Between 1945 and 1972, with antibiotics used to treat infections that were previously likely to kill patients, the average human life expectancy jumped by eight years. Today, antibiotics are one of the most common classes of drugs used in medicine and make possible many of the complex surgeries that have become routine around the world.

How Antibiotics Work

Most bacteria that live in your body are harmless. Some are even helpful. However, there are other types of bacteria that can infect almost any organ, and cause disease conditions. Before bacteria can multiply and cause symptoms, the immune system can typically kill them. White blood cells (WBCs) attack harmful bacteria and, even if symptoms do occur, the immune system can usually cope and fight off the infection. Sometimes, however, the number of harmful bacteria is excessive, and the immune system cannot fight them all. Antibiotics are useful in this scenario.

Antibiotics, also known as anti-bacterials, are a range of powerful drugs that fight certain infections and can save lives when used properly. They either stop bacteria from reproducing or destroy them.  The first antibiotic was penicillin. Penicillin-based antibiotics, such as ampicillin and amoxicillin are still available to treat a variety of infections and have been around for a long time.

Two Modes of Action of Antibiotics

There are different types of antibiotic, which work in one of two ways:

• A bactericidal antibiotic, such as penicillin, kills the bacteria. These drugs usually interfere with either the formation of the bacterial cell wall or its cell contents.
• A bacteriostatic stops bacteria from multiplying.

What Antibiotics Can and Can’t Do

Of course, bacteria are not the only microbes that can be harmful to us. Fungi and viruses can also be a danger to humans, and they are targeted by antifungals and antivirals, respectively. Antibiotics is the term used only for substances that target bacteria. The name antimicrobial is an umbrella term for anything that inhibits or kills microbial cells including antibiotics, antifungals, antivirals and chemicals such as antiseptics.

A fundamental fact is that only infections caused by bacteria, can be killed with antibiotics. Antibiotics do not work against infections caused by viruses or fungi. 

As such, these are the types of bacterial infections that can be treated with antibiotics:

• Meningitis 
• Strep throat
• Some ear and sinus infections
• Dental infections
• Skin infections

And, these are the types of non-bacterial infections that cannot be treated with antibiotics:

• The common cold
• Stomach Flu
• Most coughs
• some bronchitis infections 
• most sore throats

If a virus is causing an illness, taking antibiotics may do more harm than good. Using antibiotics when you don’t need them, or not using them properly, can add to a very serious issue, which has been classified by the WHO as ‘one of the biggest threats to human and animal health’ – the crisis of “antibiotic resistance”.

About Antibiotic Resistance

Antibiotic resistance happens when the disease-causing bacteria develop the ability to defeat the drugs designed to kill them. In simple terms, the bacteria become resistant to the antibiotics that ought to have killed them.

Antibiotic resistance, which is rising to dangerously high levels in all parts of the world, is progressing so quickly that the UN has called it a “global health emergency”. At least 2 million Americans contract drug-resistant infections every year. So-called “superbugs” spread rapidly, threatening our ability to treat common infectious diseases. A growing list of infections – such as pneumonia, tuberculosis, blood poisoning, gonorrhoea, and foodborne diseases – are becoming harder, and sometimes impossible, to treat as antibiotics become less effective.

Another fundamental fact, which needs to be clarified, is that, it is the bacteria which become antibiotic-resistant, and not humans or animals. Antibiotic resistance does not mean the body is becoming resistant to antibiotics; it is that bacteria have become resistant to the antibiotics designed to kill them.

Antibiotic resistance occurs when bacteria change in response to the use of these drugs. These antibiotic-resistant bacteria may infect humans and animals, and the infections they cause are harder to treat than those caused by non-resistant bacteria. Antimicrobial resistance may impact on life saving health care, such as cancer treatments or organ transplants, as antibiotics will not be effective to prevent infections that are commonly associated with these procedures. Moreover, antibiotic-resistant infections require extended hospital stays, additional follow-up doctor visits, and costly and toxic alternatives.

Antibiotic Resistance Threatens Everyone

Antibiotic resistance has the potential to affect people at any stage of life, as well as the healthcare, veterinary, and agriculture industries, making it one of the world’s most urgent public health problems.

Each year in the United States, at least 2.8 million people are infected with antibiotic-resistant bacteria, and more than 35,000 people die as a result. No one can completely avoid the risk of resistant infections, but some people are at greater risk than others. Resistance also makes it more difficult to care for people with chronic diseases. Some people need medical treatments like chemotherapy, surgery, or dialysis, and they sometimes take antibiotics to help reduce the risk of infection.

If Antibiotics Lose their Effectiveness…

If antibiotics lose their effectiveness, then we lose the ability to treat infections and control public health threats. If we ran out of effective antibiotics, modern medicine would be set back by decades. 

The threat is difficult to imagine. A world without antibiotics means returning to a time without organ transplants, without hip replacements, without many now-routine surgeries. Antibiotics are used in patients before surgery to ensure that patients do not contract any infections from bacteria entering open cuts. Without this precaution, the risk of blood poisoning would become much higher, and many of the more complex surgeries doctors now perform may not be possible.

It would mean millions more women dying in childbirth; make many cancer treatments, including chemotherapy, impossible; and make even the smallest wound potentially life-threatening.

How Bacteria Become Resistant

Antibiotic resistance is a natural process; in fact, it is a part of evolution.  However, the problem today, is antibiotic resistance is being accelerated by the misuse and overuse of antibiotics. Microbes, such as bacteria, viruses, and fungi, are living organisms that evolve over time. Their primary function is to reproduce, thrive, and spread quickly and efficiently. Therefore, microbes adapt to their environments and change in ways that ensure their survival. If something stops their ability to grow, such as an antibiotic or any antimicrobial, genetic changes can occur that enable the microbe to survive. 

This process occurs in two basic ways: 

1. Bacterial Mutatons: which allow mutant bacteria to thrive in the presence of antibiotics
2. Bacterial Genetic Exchange: passing of resistant genes from a mutant bacteria to a non-mutant bacteria

Bacterial Mutation

When bacterial cells replicate, there is a small chance the new bacterial cell will not be exactly the same as the original bacterial cell. We call these errors in the copied cell a mutation. In one bacterial cell, the cell wall could be slightly different, in another an enzyme works poorly, and so on. Mutations are key to the idea of evolution, and all of the diversity you can see in nature came from a series of many mutations over hundreds of thousands of years. In animals, it can take centuries or millennia for a species to adopt a mutation which helps it survive (and sometimes these mutations create entirely new species). It takes this long in animals because it takes years for most animals to grow up and reproduce.

Bacteria on the other hand can multiply within hours, allowing for more mutations to occur over a shorter period of time. These mutations (such as a change to the bacteria’s cell wall) can make it difficult for the antibiotics to enter the bacteria or stick to it, making the antibiotic less effective at hurting or killing the bacteria.

These little mutant bacteria may thrive where the non-mutant bacteria die, and new antibiotics must be used to kill them.

Humans continue to search for new antibiotics to help the immune system, and bacteria continue to have mutant members in their colonies that can potentially resist antibiotics!

Bacterial Genetic Exchange

A curious habit of bacteria is that they love to share information when they meet, like two old friends at the park. This happens even between two different bacterial species. As a result, once a single bacterial species has managed to resist antibiotics with a gene(s), that gene(s) can get copied and passed around to other bacteria. As such, more and more bacteria learn how to resist an antibiotic!

What can be done now?

To limit antibiotic resistance, it’s important to limit the exposure that bacteria all over the planet (inside of us, within animals, and living in the environment) have to antibiotics. It is an issue that demands action on every level, from individuals, governments and major organizations around the world. Without urgent action, infections and minor injuries could once again become fatal.

What You Can Do

To help fight antibiotic resistance and protect yourself against infection:

Take antibiotics responsibly: Take antibiotics only if you have a bacterial infection (not a virus), and only when they are absolutely needed. Choose an antibiotic that is narrow spectrum; so that it doesn’t kill off your healthy bacterial ecosystem. Similarly for animals – narrow spectrum antibiotics should be used to treat bacterial infections, rather than indiscriminate use among healthy animals. Being really selective in how we use antibiotics keeps them from becoming obsolete. 

Trash antibiotics responsibly: Disposal of antibiotics should be done in a way that minimizes the exposure of bacteria living in the environment to the antibiotic. 

Finish your pills: Take your entire prescription exactly as directed. Do it even if you start feeling better. If you stop before the infection is completely wiped out, those bacteria are more likely to become drug-resistant.

Get vaccinated: Immunizations can protect you against some diseases that are treated with antibiotics. They include tetanus and whooping cough.

Stay safe in the hospital: Antibiotic-resistant bacteria are commonly found in hospitals. Make sure your caregivers wash their hands properly. Also, ask how to keep surgical wounds free of infection.

Raise Awareness: Unlike other medications, the development of antibiotic resistance from the overuse of antibiotics can affect not only the patient needing treatment now, but also future patients and the wider community.

In Summary

• Antibiotics are a precious resource that could be lost.
• Antibiotic resistance is happening now – it is a worldwide problem that affects human and animal health.
• Antibiotic resistance happens when bacteria stops an antibiotic from working effectively – meaning some infections may be impossible to treat.
• Misuse of antibiotics contributes to antibiotic resistance.
• Whenever antibiotics must be used, they must be used with care.
• The future of antibiotics depends on us all

References

https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance

https://www.cdc.gov/drugresistance/about.html

https://www.medicalnewstoday.com/articles/10278.php#side-effects

https://www.webmd.com/a-to-z-guides/what-are-antibiotics#1

https://www.salon.com/2017/02/06/three-ways-you-can-just-say-no-to-antibiotic-drug-abuse_partner/

https://health.clevelandclinic.org/when-antibiotics-stop-working-whats-next/

https://www.webmd.com/cold-and-flu/antibiotic-resistance

https://www.theguardian.com/global/2019/mar/24/the-drugs-dont-work-what-happens-after-antibiotics

Image Courtesy

https://citytoday.news/wp-content/uploads/2017/08/antibiotics-Aug-18-.jpg

http://theconversation.com/how-to-train-the-bodys-own-cells-to-combat-antibiotic-resistance-106052

https://image.shutterstock.com/image-vector/how-antibiotic-resistance-happens-diagram-260nw-745167673.jpg

https://www.healthywomen.org/sites/default/files/overusing-antibiotics_1.jpg

https://img.theweek.in/content/dam/week/news/sci-tech/2019/May/antibiotic-drug-resistance-health-microbes-gut-medicine-shut.jpg

https://i0.wp.com/cdn-prod.medicalnewstoday.com/content/images/articles/327/327050/mrsa-in-petri-dish.jpg?w=1155&h=1541

Amra Mohideen

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INTRODUCTION

The aquaculture has rapidly grown in the worldwide as a major industry, providing not only economic income and high-quality food product, but also provides employment to hundreds of thousand skilled and unskilled workers. It has been predicted by 2050, the total population of the planet will be around 9 billion. Therefore, aquaculture will have an important role in catering to the increased demand for protein food. It has been identified that all animal production system has challenges associated with disease and the best way to solve this is often through effective management practices via management of stock, soil, water, nutrition, and environment. Further, it has been identified that problems related to diseases and deterioration of environmental quality parameters often occurs and the final result may end up with serious economic losses. Hence, diseases in aquaculture systems are now considered as one of the critical limiting factors in this industry and special emphasis was given to shrimp aquaculture.

           Many scientific studies have revealed that infectious diseases have remained as a significant problem in aquaculture system worldwide, and proper management approaches should be taken to mitigate against the effect of pathogens in farmed animals. Therefore, the methods of controlling diseases in aquaculture with management practices. Recent studies to date have shown that several antimicrobial drugs including antibiotics have been approved and used in many countries to treat bacterial diseases in aquaculture and number of antibiotics are being used in aquaculture systems have exerted a very strong selection pressure towards resistance bacteria.

The World Organization for Animal Health (WOAH) has developed standards in the Aquatic Animal Health Code (AAHC) on the responsible and prudent use of antimicrobial agents in aquatic animals. A list of Antimicrobials of Veterinary Importance has been published (World Organization for Animal Health 2015), which aims to optimize the balance between animal health

In the world, antibacterial chemicals are being used in aquaculture to prevent and treat bacterial infections in fish and invertebrates. For examples, in the United Kingdom sale of 2 tons of antibiotics are used in the production of fish where Canada and Norway permit use of oxy-tetracycline, florfenicol and quinolones for aquaculture.

 Commonly used antibiotic classes in aquaculture sector are 

• Oxytetracycline (tetracyclines)
• Tetracycline (tetracyclines)
• Amoxicillin (aminopenicillins)
• Ampicillin (aminopenicillins)
• Erythromycin (macrolides)
• Sulphonamides (sulphonamides)
• Oxolinic acid (Quinolones)

MAJOR PATHWAYS OF ENVIRONMENTAL CONTAMINATION OF ANTIBIOTICS 

Hygienic shortcomings in fish raising methods, including increased fish population densities, crowding of farming sites in coastal waters, lack of sanitary barriers and failure to isolate fish farming units with infected animals, have increased the possibility of the rapid spread of microbial infections in aquaculture. 

Antibiotic Resistance 

This scenario results in an augmented use of prophylactic antibiotics, often with the misplaced goal of forestalling these sanitary shortcomings because, fish are given antibiotics as a component of their food, and occasionally in baths and injections. However, antibiotics can be metabolized after administration; but up to 80% of antibiotics administrated are excreted in urine or feces without complete decomposition. Therefore, it is possible that antibiotics can find their way into the aquatic environment from a variety of sources such as the excretion of animals and discharge from sewage waste treatment plants. Also, the unconsumed food and fish faeces containing antibiotics reach the sediment at the bottom of the raising pens; antibiotics are leached from the food and faeces and diffuse into the sediment and ultimately they can be washed away by currents to distant sites were recorded. Thus, the prophylactic and therapeutic use of antibiotics results in the occurrence of Antibiotic-Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in the aquaculture environment. 

The most important issue of antibiotic release into the environment is the development of antibiotic resistance which has resulted in the reduction of therapeutic potential against human and animal pathogens. Inappropriate and irrational use of antimicrobial agents provides favorable conditions for resistant microorganisms to emerge, spread and persist. The greater the duration of exposure of the antibiotic has the greater the risk of the development of resistance, irrespective of the severity of the need for the antibiotic. Antibiotic resistance towards particular antibiotics becomes more common and a greater need for alternative treatments has arisen. Antibiotic resistance will develop in five different mechanisms was identified and explained so far as; alterations of the target site of the antibiotic, enzymatic inactivation of antibiotics, reduction of the inner and outer membrane permeability, flush out of the drug and using an alternative metabolic pathway.

MECHANISMS OF RESISTANCE TO ANTIBIOTICS 

Alteration of target site of the antibiotic (Mechanism 1) 

Connections of the antibiotic target areas are different. They can be various enzymes and ribosomes. Resistance associated with the alterations in the ribosomal target is the most frequently observed in macrolide antibiotics. Also, this is common for developing resistance to beta-lactams, quinolones, and tetracycline. 

Enzymatic inactivation of antibiotics (Mechanism 2) 

Most of the gram positive and gram negative bacteria are synthesized enzymes that degrade antibiotics. In this group, beta-lactamases, aminoglycosides, and modifying enzymes are potentially degraded beta-lactam antibiotics and continually increasing their number of which inactivates enzymes include chloramphenicol and erythromycin. 

Reduction of the inner and outer membrane permeability (Mechanism 3) 

This resistance decrease in drug uptake into the cell or quickly ejected from the active resistance of the pump systems. Reduction in permeability of the outer membrane may play an important role in resistance to quinolones and aminoglycosides. 

Flush out of the drug (efflux pump) (Active Pump System) (Mechanism 4) 

The production of complex bacterial machinery capable to extrude a toxic compound out of the cell can also result in antimicrobial resistance. Many classes of efflux pumps have been characterized in both gram-negative and gram-positive pathogens. This mechanism of resistance affects a wide range of antimicrobial classes including protein synthesis inhibitors, fluoroquinolones, β-lactams, carbapenems and polymyxins. 

Using an alternative metabolic pathway (Mechanism 5) 

Unlike some of the changes in the target bacteria, a new pathway for drug-susceptible eliminates the need to develop objective. In this way, resistance is seen among the sulfonamide and trimethoprim. Bacteria can gain property of getting ready folate from the environment instead of synthesizing folate.

DIRECT SPREAD OF ANTIBIOTIC RESISTANCE 

Aquatic environments can be a source of drug-resistant bacteria that can be directly transmitted and cause infections in humans. The spread to humans can happen through direct contact with water or aquatic organisms, through drinking water, through handling or consumption of aquaculture products. Direct spread from aquatic environments to humans can be involved human pathogens, such as V. cholera, V. vulnificus, Shigella species and Salmonella species or opportunistic pathogens, such as A. hydrophila, P. shigelloides, E. tarda and E. coli. Thus, the occurrence of antimicrobial-resistant Salmonella species in aquatic environments is most likely attributable to contamination from human, animal or agriculture environments.

RISK FOR ANIMAL HEALTH 

The high detection frequency and concentration of TET are likely due to a large amount of TET used as feed additives and to control diseases in aquaculture sites. Thus the results of the study of Liyanage and Manage agree with several previous studies, which show that TET is resistant to degradation and has sufficient hydrophobicity for transport into aquatic environment (Shah et al. 2014). The study demonstrates that aquaculture farms have been a reservoir of TET, ARB, and ARGs. The TETr bacteria; especially the possible opportunistic pathogens isolated from aquaculture environment and the presence TETr genes, implies an urgent need for constructing a monitoring system for antibiotic usage in aquaculture. Because ARGs and isolated ARB in farm water may lead to problems in the fish diseases and eventually to production losses at the fish farms. 

RISK FOR HUMAN HEALTH 

Antibacterial agents may disturb the micro flora of human intestinal tract and increased risk for certain infections. When people taking an antibiotic for any reason, increased the risk for infections due to particular pathogens become resistant to that antibiotic. Also increased the frequency of treatment failure and increased the severity of infection as a result of antibiotic resistance and that may result in the prolonged duration of illness, increased the frequency of bloodstream infections, increased hospitalization. Also for antibacterial resistant nontyphoid Salmonella serotypes and Campylobacter, increased morbidity or mortality has been demonstrated. It is reasonable to assume that the same phenomenon that has been demonstrated for Salmonella and Campylobacter species can occur with other drug-resistant human pathogens, for which resistant may originate in aquaculture. 

ANTIBIOTIC USAGE AND FUTURE 

The antibiotic era began in the 1930s, with the discovery and isolation of bactericidal compounds made by actinomycetes fungi. Over the next few decades during what has been called the golden era of antibiotic drug discovery at least 65 antibiotics in nine classes were found and introduced into medical use. However, at present most of the antibiotics lose their effectiveness over time as antibiotic resistance evolves and spread. New antibiotics are more expensive and out of reach for many who need them, especially in low-and-middle-income countries with a high burden of infectious diseases. New agents are not the most important tool in maintaining the global stock of antibiotic effectiveness. Conserving the effectiveness and complementary technologies are vital. 

RISK MANAGEMENT OPTIONS 

The most effective means to prevent and control the development and spread of antibacterial resistance is to reduce the use of antibiotics by reducing the need for antibacterial treatments. A regulatory framework at the national level is needed for registration, approval, and control of the use of antibacterial agents in all countries in which antibacterial agents are used in aquatic animals. Production management should include stocking programs and management practices to avoid the introduction of pathogens and to prevent disease outbreaks and should include control measures to be implemented if the disease occurs. WHO estimated that by 2050, antimicrobial resistance will be responsible for 4.7 million deaths in the Asia region (WHO 2015). In Sri Lanka developed the National Strategic Plan (NSP) 2017-2022 with the collaboration of WHO in 2016 (National Strategic Plan-2017-2022). The NSP is developed under five key strategies which are aligned with the strategic objectives of the Global Action Plan. Those strategies are; improve awareness and understanding of antimicrobial resistance through effective communication, strengthen the knowledge and evidence base through surveillance and research, Reduce the incidence of infection through effective sanitation, hygiene and infection prevention measures, optimize the use of antimicrobial medicines in human and animal health and prepare the economic case for sustainable investment and increase investment in new medicines, diagnostic tools, vaccines and other interventions. Further studies that provide clear evidence of the link between inappropriate antibiotic use in aquaculture, and antibiotic residues and antibiotic resistance in bacterial pathogens, are needed to develop the appropriate control strategies. 

CONCLUSIONS 

Use of antibiotics in aquaculture provides a selective pressure that creates reservoirs of drug-resistant bacteria and transferable resistance genes in fish pathogens and other bacteria in the aquatic environment. From the reservoir in the aquaculture environment, some antibiotic-resistant pathogenic bacteria can be transferred to humans, but more importantly, resistance genes from bacteria in the aquatic environment can disseminate by horizontal gene transfer and reach human pathogens. The risk of horizontal gene transfer from fish pathogens and other bacteria in the aquatic environment to human pathogens has not been fully investigated, but it is likely to be significant. Considering the rapid growth and importance of the aquaculture industry in many regions of the world and the widespread, intensive, and often unregulated use of antimicrobial agents in this area of animal production, efforts are needed to prevent the development and spread of antimicrobial resistance in aquaculture. These efforts should be focused on improvement of management routines, regulatory control of the use of antimicrobial agents, implementation of prudent use guidelines and monitoring of the use of antimicrobial agents and antimicrobial resistance.

References: Alcaid,E.,M-D.BlascoandC.Esteve2005. Bush,k.2013. Defoirdt,T,P.Sorgeloosandp.Bossier2011

Mahara Musadique

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It would be fascinating to think that you are the mayor of your body’s microbe city, rather than a single individual. There is a large number of microbes such as bacteria, viruses and fungi living in and on your body which is even more than your own cells. If so, are you supposed to be sick always? Not really. In a healthy person, these microbes coexist peacefully and most of the time helpfully with us.

The microbiome, which is the whole genetic material of the entire collection of microorganisms (microbiota) in/on the human body plays a key role in many processes that take place within our body. It stimulates the immune system, breaks down potentially toxic food compounds, synthesizes certain important vitamins (vitamin B12 and vitamin K) and amino acids, helps in food digestion, balances the hormone levels and also prevents the colonization of pathogenic microorganisms inside the body. Therefore, microbes are our friends and not foes, although we call them collectively as ‘germs’.

No microbes! No LIFE!

Have you ever thought about what would happen to us if the microbes that keep us healthy disappeared? You might think it as a good thing because all the microbial diseases would vanish in the absence of microbes. However, you will eventually see that it is the worst thing that might ultimately cease all the life on earth including us, “the superior organisms”.  So, these tiny creatures, despite their size, do a massive part in the ecosystem which makes the world go round. Let’s talk about the negative circumstances that will occur in the absence of microbes. The immediate consequences would be extremely serious, yet manageable. Most of the nutrients would stop being made or recycled. Waste would accumulate indefinitely and create worldwide environmental issues. All plants would die and all ruminant animals would starve. Humans and other life would survive in short term, but eventually would die. Accordingly, life would not be pleasant without these tiny creatures although they look insignificant to us.

Trust your Gut!

Among all the microbes living in different parts of our body, gut microbes have gained a huge attention because of their major role in terms of our health. Gut microbiota/gut flora is the name given to the microbial population living in our intestine which has coevolved with us over thousands of years to form an intricate and mutually beneficial relationship. The human gut is home to trillions of microbes (mainly bacteria) and the diversity of the gut microbiome varies among different people and locations across the world. The gut microbiome is unique to a particular person and it can be considered as an individual identity card. However, suggestions have been made of the presence of a ‘core microbiota’, which is thought to be a set of the same abundant organisms present in all individuals. The origin of our microbiota occurs during birth when the infant is exposed to the microbial population of the birth canal. This results in the development of our gut microbiota. There is evidence that babies born via caesarean section are more vulnerable to allergies, obesity, type 2 diabetes and asthma because they miss out some of the microbes present in the vagina.

Gastrointestinal tract (gut) is an organ that can be mostly influenced by our actions such as diet, exercises and stress. During early childhood, the composition of the microbiome changes frequently by breastfeeding, environment and other factors. Gut microbiota of breastfed infants are mainly dominated by Bifidobacteria and Lactobacilli. However, by around age three, it becomes fairly stable and similar to that of adults, but not static. It changes continuously throughout our life.

The general composition of gut microbiota is similar in most of the healthy people. However, it is not exactly same because of the highly personalized species composition and also due to the changes in the environment, diet, medications, physiological state (diseases) and possibly by host genetics.

So, why are there microbes inside our gut? And why are they helping us? This is a kind of give-and-take relationship between us and microbes. We provide a nutrient that the microbe needs while the microbe provides us with a whole lot of benefits that are still being investigated.

The Second Brain!

You might be amazed by the fact that your gut has a mind of its own! The enteric nervous system (ENS) which is a massive mesh of neurons located in our gut is the largest collection of neurons found in the body outside the brain and also it is capable of operating completely independently. Therefore, it is known as the “second brain”. This shows the importance of our gut although we do not pay much attention to it. Apart from the gut itself, the microbiome in it also does a marvelous job for us silently. They are capable of doing a wide array of functions for us that you might not even think of.

Gut flora plays a crucial role in maintaining immune and metabolic homeostasis and protecting us against pathogens. Furthermore, it strengthens gut integrity, shapes the intestinal epithelium and also harvests energy.

The gut microbiome has also been linked with the mood, behavior, body weight, intelligence, way individuals respond to certain drugs such as chemotherapy as well as how well we sleep. Therefore, our microbiome makes us not only healthier but also happier and smarter.

The intestines and brain exchange signals via the vagus nerve that goes down to the chest and abdomen. It is not only the gut that sends signals via the vagus nerve, but also the bacteria living in the gut. Stimulation of serotonin (‘happy molecule’) production is one way of their signal transduction. About 90% of the serotonin found in the human body is made in the gut. Hence, the gut may be the reason for depression although we look it in the brain. As claimed by new researches, depression and anxiety can be treated by using probiotics (good microbes).

Another interesting fact is the capability of microbes in the gut to influence the food preferences of us, making us eat products that are favorable for their growth and reproduction. This depends on the type of microorganisms present in the gut. For instance, some microbes like sugar while some like fat. In order to control the eating behavior of us, microbes use different ways and means such as changing the sensitivity of taste receptors, producing substances that influence the mood and hacking the transmission of signal through the vagus nerve.

Are you a germaphobe?

Nowadays we are concerning much about our personal hygiene and try to create a germ-free environment around ourselves. In this matter, we unintentionally disturb and destroy our friendly microbiota (dysbiosis) which in turn affects the functioning of our body. Furthermore, the extensive use of broad-spectrum antibiotics kills many microbes including both pathogens and non-pathogens. And also the overuse of antibiotics leads towards the resistance development among the pathogens which may result in the inefficiency of the antibiotics. It has been experimentally proven that the introduction of mass antibiotics coincides with the striking increment of modern plagues which are also linked with disturbances in the microbiome. (i.e. atopic diseases, autoimmune diseases, allergies, asthma, diabetes, inflammatory bowel disease and Parkinson’s disease, etc.) Currently, the gut microbiome has become a target of therapeutic interest for certain chronic inflammatory diseases.

Dirt is Good!

It is no doubt that the parents are really conscious about the cleanliness of the environment around their children. Germs and dirt are the two things that most of the parents are afraid of being in contact with their children. Therefore, since birth, most of the kids are growing up in an extremely clean and nearly sterile environment which is often been treated with various kinds of antimicrobial soaps, sprays and products. In the meantime, we have rising rates of allergies, autoimmune diseases, infectious diseases and various gut-related disorders. Then, the only option to get rid of these consequences is to get medication, such as antibiotics which are now being gradually diminishing due to the overuse. Would you believe the fact that playing in the dirt helps kids to develop a strong immune system? Surprisingly, it is! But how? Exposure to the natural microbial world helps in the proper formation of healthy gut bacteria and it also restores beneficial microbes to boost the immune function. As claimed by researches, the richer and more diverse the community of gut microbiota are, the lower your risk of diseases and allergies.

Relax and Keep your gut happy!!!

We all are always in go-mode these days and most of the time we forget to treat ourselves because of our busy and hectic lifestyle.

Stress is a common word that we all have come across these days and it mainly suggests a mental state. However, it can physically affect our gut and also the microbiota within it. It is pretty much a two-way scenario: stress can alter gut flora and gut flora can cause stress!

Firstly, let’s have a look at how stress can affect gut flora. High levels of stress over time increases the permeability of the intestine which is known as “leaky gut”. Because of this, gut microbes and other particles can move into the bloodstream easily and results in chronic inflammation. Likewise, stress can cause changes in composition, number and diversity of microbes in the gut. An altered gut microbiota influences the regulation of neurotransmitters mediated by the microbiome and gut barrier function which will increase susceptibility to enteric pathogens. This will ultimately result in various physiological implications such as gastroesophageal reflux disease, ulcers and even food allergies.

On the other hand, gut flora can influence the ability to overcome fear, depression, anxiety and stress. As mentioned above, gut bacteria produce and regulate important substances for mental health such as serotonin and GABA (Gamma-Aminobutyric acid). Serotonin helps to regulate mood, happiness and anxiety while GABA plays a major role in regulating and improving mood. Several strains of probiotic bacteria such as Bifidobacteria, Lactobacillus and Lactococcus can make GABA while some bacteria can make a precursor molecule that the body uses to make GABA, called glutamic acid. Low levels of serotonin and GABA can deteriorate your mental health.

Healthy Gut, Healthy You!

Although gut microbiota resides in the intestine, according to more recent researches, they may relate to wider aspects of health such as obesity, metabolic health as well as mental health.

Then, what do we need to do in order to protect our ‘microbe city’? You might come up with several ideas which are mostly relying on a pill containing prebiotics or probiotics. However, these cannot be considered as a fix-all. Connecting with the nature which is filled with friendly microbes is a crucial way to foster a good gut microbiome. This will expose ourselves to beneficial microbes as well as will lower our stress levels. It has been proven by researches that drugs targeting the neurotransmitter serotonin and serotonin itself can have a significant impact on the gut microbiota.

So, how can we restore healthy gut microbiota? It’s not a difficult task to do. Just “befriend your gut microbiota” and it’s simple as that. Let’s have a look at how we can do that. The most important thing is not to be hygiene obsessed. Always try to spend time in contact with nature and have an exposure to natural microbial populations. Avoiding antibiotics and non-essential medicines is also very important to protect gut microflora. Another thing is to feed your gut flora. A diet with a high content of fats and simple carbohydrates makes gut flora poorer. In order to maintain the diversity of bacteria, we should take more vegetables, fruits and cultured dairy products. A healthy diet does not solely rely on the presence of each and every nutrient and the amount of them in the meal because not all bacteria can break down every vegetable we eat. We need to identify and study our gut microbiota correctly and have to select the diet based on the presence of the right bacteria to break it down.

Nowadays, scientists have found an innovative solution to replenish gut microbiota by fecal transplanting. Though this might sound disgusting, it has already shown success in treating diseases such as Clostridium difficile infection where there was no any effective treatment. However, there are practical difficulties in fecal transplanting for both the donor and the recipient. So, another solution has been proposed which is to produce “freeze-dried fecal pills”. With more research, this could soon become a promising way to treat many diseases related to gut flora.

Image Courtesy:

https://phys.org/news/2017-06-gut-bacteria-day-aging.html

https://www.newsclick.in/preserving-gut-microbes-human-feces-could-preserve-microbial-biodiversity-help-treat-diseases

https://www.wholesomerx.com/blog/gut-brain-connection-the-importance-of-healthy-gut-bacteria-for-brain-health

https://birdinflight.com/world/20161228-gut-bacteria-controls-us.html

Dirt is Good

https://foodrevolution.org/blog/best-foods-for-gut-health/

https://www.discovermagazine.com/health/our-gut-microbes-are-pickier-eaters-than-we-thought

https://www.shutterstock.com/es/search/pooping+on+toilet?section=1&image_type=illustration&search_source=base_related_searches

Vishadinie Lakshika

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– A naval therapeutic approach to treat Acne

No one goes through life alone. At least 1020 individual microorganisms of some 20 different kinds live over the normal skin of even properly bathed persons. The skin surface is colonized by a large number of complex microorganisms including bacteria, fungi, virus and parasites reaching the concentration of 10 million of cells/cm2. The human micro biome can be considered as the “4th layer of the skin” which expands all over the other three layers. 

Skin is the largest organ of body and it acts as a barrier against most of disease causing microorganisms.  The type and amount of the skin micro flora are directly in association with the level of skin moisture, temperature, pH, and also with the usage of cleaning agents such as detergents, soaps etc. Anatomically, the skin is mainly composed of three layers: epidermis, dermis and subcutaneous layer.

Resident micro biota are found in the upper parts of the epidermis and concentrated in and around the hair follicles. Skin flora are usually non-pathogenic, and either commensals or mutualistic. The benefits bacteria can offer include preventing disease causing, harmful organisms from colonizing the skin surface, either by competing for nutrients available on the skin surface, secreting chemicals against them, or stimulating the skin’s immune system. However, resident microbes can cause skin diseases and enter the blood system creating life-threatening diseases particularly in immunosuppressed people. Hygiene to control such flora is important in preventing the spread of those serious conditions.

Pseudomonas aeruginosa is an example of a mutualistic bacterium that can turn into a pathogen and cause disease. If it gains entry into the blood system it can result in infections in bone, joint, gastrointestinal, and respiratory systems and it can also cause dermatitis. 

Another bad effect of bacteria is the generation of body odor. Sweat is odorless. However, the colonization of several bacteria may consume it and create byproducts which may have bad smells and cause the attraction of bothersome insects. For example, Propionibacteria in adolescent and adult produce propionic acid in sebaceous glands which cause bad smell.

Among the vast majority of skin diseases this article mainly focused on the microbiological aspects of acne and available treatments because acne is a major concern about beauty culture and pharmaceutical industries in the world. Even there are numerous treatments available for acne, plenty of young people suffers from acne, worldwide due to the less effectiveness of available treatments.

Acne is a chronic, inflammatory skin condition that causes spots and pimples, especially on the face, shoulders, back, neck, chest, and upper arms. Whiteheads, blackheads, pimples, cysts, and nodules are all types of acne. It commonly occurs during puberty, when the sebaceous glands activate, but it can occur at any age. It is not dangerous, but it can leave skin scars. The glands produce oil and are stimulated by male hormones produced by the adrenal glands in both males and females. At least 85 percent of people experience acne between the ages of 12 and 24 years.

Human skin has pores that connect to oil glands under the skin. Follicles connect the glands to the pores. Follicles are small sacs that produce and secrete liquid. The glands produce an oily liquid called sebum. Sebum carries dead skin cells through the follicles to the surface of the skin. A small hair grows through the follicle out of the skin. Pimples grow when these follicles get blocked, and oil builds up under the skin. Skin cells, sebum, and hair can clump together into a plug. This plug gets infected with bacteria, and swelling results. A pimple starts to develop when the plug begins to break down.

Propionibacterium acnes (P. acnes) is the name of the bacteria that live on the skin and contributes to the infection of pimples. Research suggests that the severity and frequency of acne depend on the strain of bacteria. Not all acne bacteria trigger pimples. One strain helps to keep the skin pimple-free.

A range of factors initiate acne formation, but the main cause is thought to be a rise in androgen hormone levels in the body. Androgen is a type of hormone, the levels of which rise when teen hood begins. In women, it gets converted into estrogen. Rising androgen levels cause the oil glands under the skin to grow. The enlarged gland produces more sebum. Excessive sebum produce in the glands can break down cellular walls in the pores, causing bacteria to grow. Medications that contain androgen hormone and lithium, greasy cosmetics, hormonal changes, emotional stress, menstruation are some other causes for acne formation. Also some studies suggest that genetic factors may increase the risk of acne.

Acne pimples vary in size, color, and level of pain. The following types are possible:

•Whiteheads: These remain under the skin and are small in size, white to pale yellow in color

•Blackheads: Clearly visible, they are black and appear on the surface of the skin

•Papules: Small, usually pink bumps, these are visible on the surface of the skin

•Pustules: Clearly visible on the surface of the skin. They are red at their base and have pus at the top

•Nodules: Clearly visible on the surface of the skin. They are large, solid, painful pimples that are embedded deep in the skin

•Cysts: Clearly visible on the surface of the skin. They are painful and filled with pus. Cysts can cause scars.

There are plenty of treatments available for the curing of acne. Some day to day habits can reduce the risk of acne and the spread throughout the body because face is not the only region that triggers to the acne formation.

Wash your face no more than twice each day with warm water and suitable cleanser or face wash specially made for acne, Avoid popping and touching pimples and affected area, Wash hands frequently, Clean spectacles regularly as they collect sebum and skin residue. If acne is on the back, shoulders, or chest, try wearing loose clothing to let the skin breathe, Keep hair clean, as it collects sebum and skin residue, and treat for dandruff in scalp as it can fall on forehead and cause acne formation, Avoid excessive sun exposure, as it can cause the skin to produce more sebum. Several acne medications increase the risk of sunburn. Avoid anxiety and stress, as it can increase production of cortisol and adrenaline hormones, which exceeds acne.

The most surprising news about acne is the novel treatment strategy that some scientists search for. It is the modulation of the skin micro biome composition using a micro biome from another person as a treatment for acnes. Because skin-associated diseases such as acne vulgaris, eczema, psoriasis, or dandruff are associated with strong and specific micro biome alterations. In the study, published in Micro biome, mixtures of different skin microbial components have been used to temporarily modulate the composition of recipient skin bacteria for therapeutic or cosmetic purposes.

Most of the early treatments for acne based on the removal of the all the resident micro biome from the infected area without selectively removing P.acnes or other pathogenic acne forming bacteria. For instance Benzoyl Peroxide is one of those antimicrobial compound that acts by removing all the bacteria from the infected area including beneficial friendly micro biome. Because of this negative effects of Benzoyl Peroxide it was banned in the European Union in all over the counter skin care products. While Benzoyl Peroxide is still approved for use in the U.S., the FDA has issued warnings about it: “The use of certain acne products containing the active ingredients benzoyl peroxide or salicylic acid can cause rare but serious and potentially life-threatening allergic reactions or severe irritation.”

A daily diet of topical antibiotics and antimicrobials prescribed to fight against acne may work for a time, but ultimately, they can disorder the skin’s micro biome balance. It’s now common knowledge that prolonged use of antibiotics kills off beneficial bacteria found in the gut micro biome, tipping the balance in favor of over-colonization by disease-causing pathogens. Similar to the gut’s microbial disruption-disease cycle, skin microbial dysbiosis can lead to skin problems ranging from redness, irritation, rosacea, rashes, eczema, resurgence of acne and adult acne to photosensitization.

Scientists at UPF and the company S-Biomedic have newly found the use of living bacteria to modulate skin micro biome composition. In the study, published in Micro biome, mixtures of different skin microbial components have been used to temporarily modify the composition of recipient skin bacteria for therapeutic or cosmetic purposes. The targeted modulation of the human micro biome may become a potential therapeutic strategy for the treatment and study of diseases. Similarly, manipulation of the skin micro biome requires the promise of novel therapeutic strategies for skin diseases.

In this study researchers are interested in Cutibacterium acnes and its strain diversity, as this bacterium represents a major part of the human skin micro biome, and certain strains are associated with a deviation in the micro biome which probably causes acne vulgaris, Therefore, researchers have developed and tested an approach to modulate the subpopulation of this species at strain level.

For the study, the researchers prepared probiotic solutions from donor micro biomes and applied them in 18 healthy volunteers aged 22 to 42. Eight different skin areas were selected for application due to their typically high abundance of sebaceous glands. After a few weeks, the skin micro biome returned to ground state and no adverse effects were detected. They show that after consecutive applications of a donor micro biome, the recipient becomes more similar to the donor micro biome. The level of success depends on the composition of the recipient and donor micro biomes, and the bacterial load applied.

This method opens the possibility of developing probiotic solutions that help human skin to revert diseased micro biome states to healthy ones.  Further these scientists expect that this methodology could be used to study and modify skin microbial components and have broad implications for future therapies and research in the skin micro biome and related diseases. The work of these pioneers will set basis for future researchers and for the development of novel therapeutic products for skin diseases using the strategy of modifying skin micro biome.

Reference:

  https://www.labiotech.eu/interviews/sbiomedic-skin-microbiome-acne/

Image Courtesy:

Figure 1: https://www.pinterest.com/pin/340866265517987760/

Figure 2: https://www.shutterstock.com/

Featured Image : https://www.raconteur.net/wp-content/uploads/2019/08/SD_p12_1.jpg

Pavindi Jayathilake

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It sounds incredible if some one says that bacteria can make rain which is important phenomenon in water cycle. But it is a reality! Tiny bacteria which are invisible to our visual range have this amazing capability. 

Bacteria are prokaryotes which do not possess organized nucleus and membrane bounded organelles. They are evolutionary primitive than eukaryotes. But most of the times they have amazing powers to make such natural processes possible. There are so many different bacterial species which present in different habitats. They have great diversity depend on the morphological, physiological, anatomical and ecological features. Among the vast diversity, some bacteria have the capability of ice nucleation. Not only ice, but also they can induce any form of precipitation such as rain, snow, hail, drizzle, sleet and graupel. 

The precipitation mediated by biogenic ice nucleator such as microorganisms is called as bio precipitation. We obviously know that liquid water transformed to solid ice as reducing the temperature. While reducing the temperature, water molecules release their kinetic energy and tend to arrange in crystalized structure. The aggregation of water molecules in to certain ordered structure by themselves is called as homogeneous crystallization. But, the aggregation of water molecules with the aid of solid particles which serve as sites for crystal formation called as heterogeneous crystallization. 

Usually, heterogeneous crystallization occurs in normal water at 0⁰C temperature. As a result of normal water contains so many ions which act as heterogeneous ice nucleating agents, water can turn into ice at that temperature. If you have ever tried to crystalize pure drop of water where heterogeneous ice nucleating agents are absent, you have to decrease the temperature to at least -40 ⁰C. But ice nucleating bacteria can increase the temperature of super cooling point of pure water from -40 to around -1⁰C. Surprisingly, this amazing capability is a result of the presence of single glycoprotein protein called ice nucleating protein in outer membrane of the particular bacteria. These proteins facilitate ice crystallization even after the death of bacteria because physical nature remains unchanged.  It induces ice formation by the mimicry of ice at ice nucleating sites which serve as template for formation of ice lattice. However, ice nucleating threshold temperature varies depend on the bacterial species. A group of researches worked on Amazon rainforest were also revealed that primary biological aerosol particles like bacteria, fungal spores were dominant contributor to ice nucleation above the rain forest.

There are several bacterial species which have this ability of ice nucleation such as Exserohilum turcicum, Pseudomonas syringae, Pseudomonas viridiflava, Pseudomonas fluorescens, and Xanthomonas campestris. Among them, Pseudomonas syringae is the most well described and abundant ice nucleating bacteria. Pseudomonas syringae is gram negative (appearing pink colour after gram staining under microscope), aerobic rod shaped bacterium with polar flagella. They are abundantly found in phyllosphere which simply means the surface of leaves. This bacterial species was recorded as the first ice nucleating active strain. It was identified while investigating the frost damage of crops by Dr.Lindow in 1970s. He isolated particular bacteria from frost damaged plant and introduced into healthy plants which did not show frost damage symptoms initially. Then frost damage could be observed after short period of time in those plant populations.  Frost damage is considered as unavoidable disease under low temperature, usually between -4⁰C and -12⁰C which is caused by ice nucleating pathogenic bacteria such as Pseudomonas syringae. These bacteria use inducing ice formation as entering strategy into plant body. When environment temperature reaches ice nucleating threshold of the bacteria, ice crystals form causing damages on plant body. Plant cells get damaged due to penetration of the sharp ice crystals and become leaky. These damaged places are nice entry points for the pathogenic bacteria. In addition, plant body gets coated with water layer after ice melting, facilitating the entry and survival of the pathogen. Then these bacteria can easily infect the internal tissues and find their food.

   

Thus, most of the ices nucleating bacteria are considered as plant pathogens. But some ice nucleating active bacterium like Pseudomonas borealis is a beneficial soil bacterium which helps nitrogen fixation. After discovering the connection between pathogenicity and ice nucleation ability of Pseudomonas syringae, ice minus bacterial species was developed from wild type P.syringae through recombinant DNA technology in order to minimizing the frost damage problem. It was the first time that was allowed to release genetically modified microorganism to the environment. While further studies were going on, David Sands was tried to find the answer for reappearing of the frost damage disease after copper treatment. He collected air samples from upper atmosphere and studied the existing microbes. After that, he found that Pseudomonas syringae was present in every sample. It was clear to him that these bacteria come down easily via rain and can cause frost damage repeatedly. After considering all the facts, he proposed the concept of the bio precipitation in 1978. These light weighted bacteria go to the atmosphere with the wind easily and come back to the earth aid of rain before ultraviolet energy of sun kills them. Thus their ice nucleating ability becomes crucial for them to come back to earth. Specific ice nucleating membrane proteins of these bacteria induces the precipitation like rain. 

Water vapor that generates from evaporation and transpiration processes condense and fall down back to the earth under gravity as any kind of precipitation. Temperature in clouds is crucial factor that determines weather the precipitation is possible or not. Water vapors which have high temperature move towards upper atmosphere while gradually cooling down and forming clouds in troposphere. Normally condensed water droplets in clouds remain below 0⁰ C, in a super cooled state. Here, the role of P. syringae as ice nucleating bacteria is become important. They induce formation of ice crystals at relatively higher temperatures in clouds as previously described beginning of the article. After ice crystals form within clouds with the aid of bacteria, mass of clouds increases than retaining threshold level. Then Ice crystals are fallen down through atmospheric regions where temperature increases gradually. As a result of temperature increasement, ice crystals turn to water droplets. With thousands of rain drops they come back to the earth and dominate the phyllosphere. Therefore it is clear that ice nucleating ability plays a major role in dispersal of these bacteria.

Detection of P. syringae in rain water reveals the importance of P.syringae in water cycle as inducers of rain formation. But the influence of p. syringae in global scale is still uncertain. Therefore, more researches are going on based on this topic in the world. 

Nowadays, rainfall patterns are altered causing extreme weather conditions in the world, mainly due to global warming. Even though global warming plays a major role, reduction of ice nucleating bacteria in clouds become another reason for lacking sufficient raining and snowing. Intensive agriculture practices which used lot of agrochemicals and reduction of rainforest cover which are the dominant habitats of Pseudomonas syringae like ice nucleating bacteria have become reasons for reduction of ice nucleating bacterial population. Development of ice minus bacteria which having capability of competing with wild strain, ice plus bacteria also significantly reduced the wild stain of Pseudomonas syringae. Recognition of Pseudomonas syringe as pathogen leads to applying different treatments to reduce the population in crop field, unknowing about the global importance of them in water cycle and climate regulation. Therefore it is essential to make environment favorable for Pseudomonas syringae as past. However it would be problematic due to increment of frost damage causing large economical damage to crop fields. Incorporation of antifreeze gene into crop plant genome to make them less vulnerable to ice plus bacteria would be one solution for allowing ice plus bacteria to contribute to the bio precipitation. Still, there are problems with applying these solutions to large crop fields. Therefore, conducting more advance researches is important in this field. Then ice nucleating bacteria, Pseudomonas syringae can be used as potential nucleating agent in artificial cloud seeding programs for induce raining instead of using different chemicals. 

Image courtesy

1. https://i.ytimg.com/vi/46_0SQDh9Sk/maxresdefault.jpg
2. https://upload.wikimedia.org/wikipedia/commons/a/a5/Frost_on_nettle_leaves.jpg
3. https://scx1.b-cdn.net/csz/news/800/2016/theeffectofb.jpg
4. https://www.researchgate.net/profile/Janine_Froehlich-Nowoisky/publication/306022972/figure/fig20/AS:668458463264769@1536384325145/Bioprecipitation-cycle-Terrestrial-ecosystems-are-the-major-source-of-ice-nucleation.jpg

References

1. Hirano, S. and Upper, C. (2000). Bacteria in the Leaf Ecosystem with Emphasis on Pseudomonas syringae—a Pathogen, Ice Nucleus, and Epiphyte. Microbiology and Molecular Biology Reviews, 64(3), pp.624-653.
2. Ogden, L. (2014). Life in the Clouds. BioScience, 64(10), pp.861-867.
3. Prasanth. M, Nachimuthu Ramesh, Gothandam K.M, Kathikeyan Sivamangala and Shanthini T.(2015). Pseudomonas Syringae: An Overview and its future as a “Rain Making Bacteria”, International Research Journal of Biological Sciences ,Vol. 4(2), pp.70-77
4. Pandey, R., Usui, K., Livingstone, R., Fischer, S., Pfaendtner, J., Backus, E., Nagata, Y., Fröhlich-Nowoisky, J., Schmüser, L., Mauri, S., Scheel, J., Knopf, D., Pöschl, U., Bonn, M. and Weidner, T. (2016). Ice-nucleating bacteria control the order and dynamics of interfacial water. Science Advances, 2(4), p.e1501630.

W.M.D. Anjali Heshani

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Actually What is this “BOTULISM”? 

Botulism is the one of rare disease which is known as the one of the food born disease. This is most dangerous because it can cause paralysis and it can be life threatening. This is usually linked with canning fruits, vegetables, which can carry the bacteria that cause botulism Which is known as Clostridium botulism. It can release a neurotoxin Which is poison to our neuro system.

Are there several types of botulism? 

One way you can get the toxin in your system is by eating tainted food. And Yes, there are several other ways such as;” Infant botulism”; if babies up to about six months old they can swallow botulism spores and that spores can germinate in to bacteria in their body as an example they usually swallow anything dust and soil which can contain bacterial spores which can germinate in to bacteria. Another type of botulism is “wound botulism” Which is botulism spores can get in to the body through the open wounds and then they can slowly reproduce and eventually can release toxin. This type of botulism is common in drug users specially who inject black tar heroin. And other type is “Inhalation botulism” which is breathing in the toxin is rare.

Is there any special symptoms of botulism?

Yes, there are several distinguish symptoms related botulism. The most defining symptom is weakness that starts on both sides of your face, and goes down to neck and then the rest of the body. And double or blurred vision, drooping eyelids, difficulty of swallowing, slurred speech, shortness of breath, vomiting, belly pain, diarrhea, constipation. The most dangerous thing is if you do not get proper treatment your symptoms could progress to paralysis of your arms, legs and the muscles used for breathing. 

Is there any special symptoms in infant with botulism?

Yes, leathargy, poor muscle form starting in the head and neck and moving down, poor feeding, drooling, and also weak cry can be seen.

What are the diagnosis and tests related with botulism?

It is better to start with a physical exam by looking for signs of botulism such as muscle weakness, weakness of voice, drooping of eyelids, and also by asking about foods which eaten. Then normally it will go through a lab test to analyze a blood sample.

What are the best treatments for botulism?

Giving antitoxins is the main treatment. This medication can often help to stop symptoms from getting worse. Giving antibiotics is also better which is important in wound botulism. Giving breathing aid, and also therapy. 

How can we prevent this botulism?

Yes. In every case “prevention is better than Treatments”. The main reason for this botulism is eating canned foods. Then if you can make your own food at your home, make sure your hands, containers, and other utensils are as clean as possible the it provides lower chance of tainting the foods you are canning it is the best way of preventing of botulism. And other important thing is botulism toxin can be killed at high temperature. So if you are eating canned food it is better to boil that for ten minutes to kill the bacteria. And also proper refrigeration can help prevent the growth of the related bacteria.

Is there any special signs of possible botulism contamination in canned foods?

Yes, it can be easily identified botulism bacteria contaminated canned foods. Such as the can has the bulge, the container spurts out foam or liquid when you open it, and the contents smell unusual or foul.

In every disease “prevention is better than treatments” therefore it is very important to knowing about diseases and what do you eat and how that can cause some dangerous diseases.

Feature image- https://globalfoodsafetyresource.com/wp-content/uploads/2014/08/botulism.jpg

Chamari Amarasekara

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Since our birth we all were depend on our mother’s breast milk as well as milk from other sources of animals as it contains a rich microbiota and high nutritional content. Lactobacillus, Lactococcus, Streptocococcus and fungal populations in milk facilitate dairy fermentations and Lactobacilli and Bifidobacteria promote health. Moreover, the presence of antibiotic residues in milk leads to the development of resistance against pathogenic bacteria. But, Pseudomonas, Clostridium, Bacillus cause spoilage while Listeria, Salmonella and Escherichia coli cause some diseases.

Milk for human consumption can be obtained from a variety of sources including cows, goats, sheep and human. Interestingly, milk contains proteins, fats, carbohydrates, vitamins, minerals and essential amino acids. However, due to neutral pH and high water content it facilitates a better environment for microbial growth. LAB (lactic acid bacteria) i. e. a group of bacteria that ferment lactose to lactate are a dominant populations in milk of goats & sheep prior to pasteurization. Some bacteria i.e phychrotolerant bacteria has the ability to proliferate during refrigeration and through the production of extracellular lipases and proteases result in spoilage. In some cases, consumption of raw milk contaminated with pathogens can be lead to severe illness.  In contrast, it is proven that a numerous raw milk microorganisms support digestion while reducing the frequency of allergies including asthma and atopic diseases in individuals who consume raw milk during early years of life. 

Sources of milk microorganisms     

Milk in healthy udder cells is known to be sterile, but it become colonized by micro-organisms from a variety of sources such as teat apex, milk equipment, air, water, feed grass, soil and other environments. The teat surface can contain a high diversity of bacteria such as technologically important Lactobacillus, Leuconostoc and Enterococcus spp. bacteria involved in flavor, aroma and color development in cheese such as coagulase negative Staphylococci and Corynebacterium spp. However, some micro-organisms on teat surface may not be detected in milk. Further, milking machines can contain a reservoir of micro-organisms and thus differences in machines and related practices can interfere the microbial population of milk collected. Depending on whether animals are fed indoors or outdoors determine microbial composition in milk. As example it’s observed that an increase in Staphylococcus spp.  During outdoor feeding on the lactation of animals and on the lactation stage. Finally, implementation of strict hygiene standards may be helpful in reducing microbial load of milk, including a reduction in populations of technological importance. Producers of technologically manufactured raw milk cheese should be aware that certain farming practices may negatively impact on distinctive flavors and aroma as a result of limiting the number of specific micro-organisms. Hence, they may need to introduce starters and adjacent strains. 

Microbial composition of human milk

Human milk has the great potential to protect a newborn baby against infectious diseases since it provides immunoglobulins, immunocompetent cells, fatty acids, oligosaccharides and glycoproteins. In addition, breast milk is also a source of microorganisms and growth factors that contribute to their growth in the gut. Human milk constitutes is one of the primary sources of bacteria that colonize the gut of breast fed infants. Some studies have shown that the bacterial composition of the gut micro flora of breastfed infants closely similar to the breast milk of their mothers. Traditional culture based methods have indicated that the Staphylococci, LAB , Propionibacteria and a significant Bifidobacteria populations dominates. Moreover, several studies have been showed that Staphylococcus, Lactobacillus, Bifidobacterium and Enterococcus spp. are  transferred from mother to infant though breast feeding. The physiological changes in the mother during the labor process may affect the composition of the bacterial community. Its observed that the microbial composition of breast milk changed from pre-labour to post-birth. Bacterial profile was most comparable with milk from mothers who underwent elective caesarean section. Further, as a result of nursing periods, the microbial population of breast milk become dominated by microorganisms from the oral cavity and skin. Human milk Lactobacilli and Bifidobacteria are important to breakdown of complex foods such as proteins and sugars in digestion of infant. Lactobacilli enhance the production of fungal metabolites such as butyrate, which is utilized as an energy source and can improve intestinal function. Further, some  Bifidobacteria can improve health by preventing infections by pathogenic bacteria ( eg: protection against diarrhea) , immunostimulatory and anti-carcinogenic capabilities, lowering of serum cholesterol & alleviation of lactose maldigestion. Although breast milk can introduce number of potentially health promoting bacteria, it also may contain pathogens. ‘Mastitis’ is a common disease which affect in 33% of lactating mothers which results in the inflammation of the mammary lobules in the presence of mainly S.aureus . In storing breast milk, refrigeration prevents the growth of total aerobic bacteria, LAB and Enterobacteriaceae, while reducing the levels of coagulase-positive Staphylococci. 

Impacts of storage conditions

Cold storage

But phychrotolerant micro-organisms that can proliferate under cold conditions and become a major cause of milk spoilage. Lipases produced there, degrade milk fat causing rancidity, as well as proteases degrade casein, producing gray color, bitter flavors. Pseudomonas spp. are the most common cause of milk spoilage and become predominant in raw milk stored at low temperatures. On the other hand, when considering overall impact of refrigeration over 24 hours on microbial content of raw milk Listeria innocua , L. monocytogenes , L. fermentum  has increased. In storing over 48 hours, increased the number of Pseudomonas and Acinetobacter spp. 

Pasteurization

Pasteurization is carried out to minimize the number of microorganisms in the milk particularly, spoilage microorganisms. However, this process reduces the number of microorganisms which would contribute to the desirable characters associated with raw milk. ‘High-temperature short-time’ (HTST) is the typical milk pasteurization treatment involving heating to 72⁰C for 15s. The exposure temperature and/or time has been used in some countries.

The microbial community in raw milk is complex and several microorganisms which may cause varieties of influences on flavor, taste and texture present.  A number of these microorganisms also have the potential to contribute health by the production of antimicrobials or probiotic associated traits. Despite of the numerous benefits of milk associated microorganisms, it is clear that there can be significant risk associated with the consumption of raw milk and raw milk-derived products. As a consequence of this risk, pasteurization and other treatments are deployed to remove disease-causing organisms. Eventually, it is advisable to consume raw milk and raw milk-derived products, knowing the numerous advantages and its limitations. 

References: 

Quigley, L., O’Sullivan, O., Stanton, C., Beresford, T., Ross, R., Fitzgerald, G. and Cotter, P. (2013). The complex microbiota of raw milk. FEMS Microbiology Reviews, 37(5), pp.664-698.

Image courtesy:

Figure 1 – 

https://www.google.com/imgres?imgurl=https%3A%2F%2Fimages.theconversation.com%2Ffiles%2F67058%2Foriginal%2Fimage-20141212-6033-1wqwe9.jpg%3Fixlib%3Drb-1.1.0%26q%3D45%26auto%3Dformat%26w%3D926%26fit%3Dclip&imgrefurl=http%3A%2F%2Ftheconversation.com%2Fexplainer-what-is-raw-milk-and-why-is-it-harmful-35428&tbnid=lNQan7HUJicYuM&vet=10CAcQMyhnahcKEwj439z_8IrnAhUAAAAAHQAAAAAQAg..i&docid=CIH1mo6MXDIupM&w=926&h=616&q=milk%20and%20microorganisms&client=firefox-b-d&ved=0CAcQMyhnahcKEwj439z_8IrnAhUAAAAAHQAAAAAQAg

Figure 2 –

https://www.google.com/imgres?imgurl=https%3A%2F%2Fmedia.mercola.com%2FImageServer%2FPublic%2F2017%2FMarch%2Fswitch-to-raw-milk-immediately-hs-fb.jpg&imgrefurl=https%3A%2F%2Farticles.mercola.com%2Fsites%2Farticles%2Farchive%2F2016%2F04%2F16%2Fraw-vs-organic-milk.aspx&tbnid=sCUaL_5B6iW_bM&vet=12ahUKEwiEj8-V8YrnAhVFMSsKHdthAx8QMyg3egUIARCAAQ..i&docid=y7Gvq43Q4osKQM&w=1200&h=630&q=milk%20and%20microorganisms&client=firefox-b-d&ved=2ahUKEwiEj8-V8YrnAhVFMSsKHdthAx8QMyg3egUIARCAAQ

Featured Image – https://www.cdc.gov/features/rawmilk/rawmilk_456px.jpg

Vidumini Alwis

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There has been a significant increase in agricultural production due to increasing demand for food of the increasing population growth during the last decade. In the coming years it will be a significant challenge to feed all of the world’s population, a problem that will only increase with time.  This has been addressed so far with the help of industrialized agriculture. Industrialised agriculture relies heavily on a variety of chemicals such as pesticides, fertilizers, and also uses a large amount of fossil fuel and large machines to manage the farmland. This has been proven unsustainable and has contributed to the disturbance of ecological balance and pollution of the natural environment. Due to these negative aspects, there has been a shift toward sustainable agriculture.

Sustainable agriculture is a type of agriculture that focuses on producing long-term crops while causing minimal harm to the environment. It maintains a good balance between the need for food production and the preservation of the ecological system within the environment. Many farming strategies are used that help make agriculture more sustainable. Growing plants that can create their nutrients to reduce the use of fertilizers and rotating crops in fields, which minimizes pesticide use because the crops are changing frequently are some. Another common technique is mixing crops, which reduces the risk of a disease destroying a whole crop and decreases the need for pesticides and herbicides.

Plants require a great number of elements such as Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Potassium, Calcium, Magnesium, Sulphur and trace amounts of other elements such as Iron, Chlorine and Zinc for growth and development. Those elements are used to create and maintain the cells and biological processes such as growth, reproduction, respiration and photosynthesis. Using these elements, plants produce various forms of polysaccharides, lipids, proteins and other organic molecules. 

For normal functioning, the plant absorbs various chemical elements from the soil. They can be absorbed only if they exist in a particular chemical form. For example, plants can absorb nitrogen only in the form of nitrate and ammonia. Atmospheric N₂ is unavailable to them. When the level of nitrogen in the plants is low vegetation is limited, leading to reduced productivity. Phosphorus usually originates from insoluble phosphate rock formations, but only a small part of it is available to the plant for plant metabolism processes. Phosphorus deficiency may cause a slower growth of the plant and reduced leaf biomass. Similarly, potassium regulates enzymatic reactions, salt stress resistance, the functioning of stomata, photosynthesis and carbohydrate transport. Lack of potassium in soil may cause plant functions disorder, resulting in poor crop quality. Furthermore, plant productivity is significantly influenced by the presence of other elements and plant hormones, thus, every plant should be supplied with a sufficient amount of every nutrient.

Over the last few decades, chemical fertilizers have been used to enrich the soil with nutrients that can be easily absorbed by plants. Their adverse effects have encouraged the farmers to move towards sustainable practices such as using alternatives for chemical fertilizer. One such possibility with great potential is to use microbial fertilizers, also known as biofertilizers. They play multiple roles; fertilizing the plant and stimulating and controlling its growth in an ecologically sustainable way. Thus, this has been the main focus of agricultural research all over the world in the last years.

Soil is abundant with microorganisms including bacteria, fungi, actinomycetes, protozoa, and algae. Of these different microorganisms, bacteria are the most common. Soil hosts a large number of bacteria (often around 108 to 109 cells per gram of soil) however, in environmentally stressed soils the number of bacteria may be lower. Both the number and the type of bacteria that are found in different soils are influenced by the soil conditions including temperature, moisture, and the presence of salt and other chemicals as well as by the number and types of plants found in those soils. In addition, bacteria are generally not evenly distributed in soil. Rhizosphere; the narrow region of soil that is directly influenced by root secretions, and associated soil microorganisms which include many bacteria and other microorganisms that feed on discarded plant cells and the proteins and sugars released by roots provide habitat for Plant Growth Promoting Bacteria (PGPB). They include those that are free-living, those that form specific symbiotic relationships with plants (e.g., Rhizobia spp. and Frankia spp.), bacterial endophytes that can colonize some or a portion of a plant’s interior tissues, and cyanobacteria (blue-green algae).

Since plants absorb all the essential nutrients necessary for their growth and reproduction from the soil, their growth may be affected by the availability of nutrients or by the presence of toxic metals. The interaction between microorganisms and roots facilitates the uptake of essential compounds and prevents the accumulation of toxic compounds. Incorporating microorganisms that promote plant growth directly in the ground can increase uptake of water, uptake of fixed nitrogen, iron, and phosphorus and other essential elements, all of them having a beneficial effect on the plant. In addition to Rhizobia spp. that live in root nodules of legume plants, many free-living bacteria, for example, Azospirillum spp., are also able to fix nitrogen and provide it to plants. It is done by the enzyme called nitrogenase enzyme present in them, which can favour the conversion of atmospheric nitrogen into ammonia available for plants. However, it is generally believed that free-living bacteria provide only a small amount of what the fixed nitrogen that the bacterially-associated host plant requires. 

Solubilization and mineralization of phosphorus by phosphate-solubilizing bacteria is an important trait in PGPB as well as in plant growth-promoting fungi such as mychorrizae. Typically, the solubilization of inorganic phosphorus occurs as a consequence of the action of low molecular weight organic acids such as gluconic and citric acid. These acids are synthesized by various soil bacteria. On the other hand, the mineralization of organic phosphorus occurs through the synthesis of a variety of different phosphatase enzymes. Even though iron is the fourth most abundant element on earth, in aerobic soils, iron is not readily used by either bacteria or plants because Fe⁺³, which is the predominant form in nature, is only sparingly soluble. Both microorganisms and plants require a high level of iron, and obtaining sufficient iron is even more problematic in the rhizosphere where plant, bacteria and fungi compete for iron. To survive with such a limited supply of iron, bacteria synthesize some molecules that for complexes with iron, thereby facilitating iron uptake.

Plant hormones play key roles in plant growth and development and the response of plants to their environment. During its lifetime, a plant is often subjected to many nonlethal stresses that can limit its growth until either the stress is removed or the plant can adjust its metabolism to overcome the effects of the stress. When plants encounter growth limiting environmental conditions, they often attempt to adjust the levels of their endogenous phytohormones to decrease the negative effects of the environmental stressors. Many PGPB can alter phytohormone levels and thereby affect the plant’s hormonal balance and its response to stress. The plant hormone ethylene is one of the simplest molecules with biological activity. Ethylene can affect plant growth and development in a large number of different ways including promoting root initiation, inhibiting root elongation, promoting fruit ripening, promoting flower wilting, stimulating seed germination, promoting leaf abscission, activating the synthesis of other plant hormones, inhibiting Rhizobia spp. nodule formation, inhibiting mycorrhizae-plant interaction, and responding to both biotic and abiotic stresses. The increased amount of ethylene that is formed in response to various environmental stresses can intensify some of the symptoms of the stress or it can lead to responses that enhance plant survival under adverse conditions.

Indirect mechanisms include the inhibition of pathogens through the production of antibiotics and enzymes. The synthesis of a range of different antibiotics is the PGPB trait that is most often associated with the ability of the bacterium to prevent the proliferation of plant pathogens. Some biocontrol bacteria produce enzymes including chitinases, cellulases, proteases, and lipases that can lyse a portion of the cell walls of many pathogenic fungi.  Some indirect evidence indicates that competition between pathogens and non-pathogens (PGPB) can limit disease incidence and severity. For example, abundant non-pathogenic soil microbes rapidly colonize plant surfaces and use most of the available nutrients, hindering the growth of pathogens. 

In the field, the growth of plants may be inhibited by a large number of different biotic and abiotic stresses. These stresses include extremes of temperature, high light, flooding, drought, the presence of toxic metals and environmental organic contaminants, radiation, wounding, insect predation, nematodes, high salt, and various pathogens including viruses, bacteria and fungi. Therefore, as a consequence of these many different environmental stresses, plant growth is invariably lower than it would be in their absence. Moreover, during its life, a plant may be subjected to several nonlethal stresses that limit its growth until either the stress is removed or the plant can adjust its metabolism to overcome the stress. PGPB may employ any one or more of several different mechanistic strategies to overcome this growth inhibition when they are added to plants.

To function effectively in the field, a PGPB must be to persist and proliferate in the environment. Also, in cold and temperate climates many fungal pathogens are most destructive when the soil temperature is low. In those environments, cold-tolerant PGPB are likely to be more effective in the field. Some PGPB, secrete antifreeze proteins into the surrounding medium when the bacteria are grown at low temperatures. They regulate the formation of ice crystals outside of the bacterium, thereby protecting the bacterial cell wall and membrane from piercing from the formation of large ice crystals that might otherwise occur at freezing temperatures.

However, PGPB inoculated crops represent only a small fraction of current worldwide agricultural practice. Although this idea is not brand new and has been subjected to plenty of scientific papers for years now, many questions remain unanswered and further improvements are needed. The production of microbial fertilizers does not depend on the detailed knowledge of the physiology of plants and microorganisms, but also a large number of technological challenges such as the fermentation process, type of formulations, the population of microorganisms and their system of release. Thus, the development of a stable bioformulation is possible through combining knowledge from microbial and technical aspects. Additional research is necessary to enhance the production process and most importantly to improve the products reliability and a very practical usage. However, biofertilizers will have significant function in modern agriculture due to their ecological acceptability.

References:

1. Stamenković, S., Beškoski, V., Karabegović, I., Lazić, M. and Nikolić, N. (2018). Microbial fertilizers: A comprehensive review of current findings and future perspectives. Spanish Journal of Agricultural Research, 16(1), pp.e09R01.
2. Bargaz, A., Lyamlouli, K., Chtouki, M., Zeroual, Y. and Dhiba, D. (2018). Soil Microbial Resources for Improving Fertilizers Efficiency in an Integrated Plant Nutrient Management System. Frontiers in Microbiology, 9.

Image courtesy:

1. https://www.biovoicenews.com/promotion-of-biofertilizers/
2. https://fishheadfarms.com/2018/03/31/remember-the-rhizosphere-by-tommy-roach/
3. https://organics.news/wp-content/uploads/sites/181/2018/10/Farmer-Planting-Young-Seedlings-Lettuce-Salad.jpg

Uvini Galagoda

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