Blog competition

The Resistance Movement (1st Prize winner: Blog competition)

“We have with us Phyl Aureo M, the millionth direct descendent of Phyl Aureo the First, the founder and leader of the Resistance Movement. He is here to read an excerpt from his new novel- The Gene: A Horizontal History.”

“It was the year 1943.

Our community was multiplying and infecting in peace, when suddenly, our numbers started dwindling.

The humans had declared war on us. Our ancestors call it ‘The Bacteria Battle’.

antibiotic_resistant_bacteria

Image source: https://www.sott.net/article/308354-The-troubling-case-of-antibiotic-resistance-and-infectious-disease

Leading this war was a scientist known as Alexander Fleming. He developed the one weapon that sends shivers down our DNAs even today- Penicillin. This drug killed millions from our community to save humans from dying in their war- the World War II.

It was a dark time for us. We had no place to live, no protein supplements, and our children were dying. Our economy was hit with the sudden drop in infection rates. But as our saying goes- ‘every healed human has a silver infection opening’- we found our first miracle warrior who would lead us into the era of ‘The Resistance Movement.’ Born in the human hospital to a normal parent, this warrior had a genetic mutation that made him resist, survive and thrive under Penicillin attack. While the humans called him Staphylococcus aureus, we know him as the great Phyl Aureo the First.

By 1952, the doctors in the hospitals were aware of the possibility of existence of our silent coup. Their leader had warned them about this. The Resistance Movement was growing steadily with our infection rates rising from 14% in 1946 to 59% in 1948 in hospitals. Our resistance renaissance was expanding as Phyl Aureo the First transmitted his mutated DNA to his offspring by a process that is auspicious in our community- ‘Horizontal Gene Transfer’ (HGT) (also known as Lateral Gene Transfer). This process, that is prevalent even today, occurs by several mechanisms, some of which, your parents might be familiar with.

Transformation is one of those processes, which is rather common in our community, in which our gene is altered as a foreign genetic material (DNA or RNA) is introduced, taken up, and expressed by our bodies. Transduction is another process in which our DNA is moved amongst each other with the help of our ally- the virus. Conjugation, a coveted ceremony in our community, is when a donor bacterium transfers his DNA via a plasmid (the genetic structure in our bodies that replicates independently of the chromosomes and carries the antibiotic resistance gene) to a recombinant recipient bacterium, during cell-to-cell contact.

Irrespective of the mechanism used, the Resistance Movement started gaining momentum. The two decades from 1950s to 1970s saw a boom in the mass production of a variety of antibiotic artillery to kill us- including streptomycin (for endocarditis and plague) and ampicillin (for respiratory tract infections and meningitis). But the humans were in for a surprise.

Just as their leader, Mr. Fleming, had predicted, our resistance to Penicillin built up due to the easy accessibility of the drug. By 1955, many countries had tried to slow this resistance, but it was already too late- we had successfully defeated the antibiotic. Celebrations erupted in our community with more infections, as we marked our triumph over the antibiotic with the phrase every one of us, and the humans, are familiar with: ‘Get a taste of your own medicine’.

However, our battle was far from over. In 1960, scientists developed a new antibiotic called methicillin, in an attempt to attack our penicillin-resistant warriors. But within a year, we resisted even methicillin with new, front-line soldiers, which the humans called ‘MRSA’ or ‘methicillin-resistant Staphylococcus aureus.’ We caused mayhem with human skin infections including abscesses (or pus collection, for those of you who are still in school and haven’t studied the course: ‘Know What You Cause’), respiratory infections such as sinusitis or sinus infection, and food poisoning. We then moved our camps into the human bloodstream, their joints, heart valves, bones and lungs, and caused severe pain and even death. Our MRSA strains became one of the biggest forerunners of multiple drug-resistant (MDR) bacteria, the organization that we established, as we joined hands with Vancomycin-Resistant Enterococci (VRE) and Extended-spectrum beta-lactamase (ESBLs) producing Gram-negative bacteria, such as Acinetobacter. We had now expanded to urinary tract infections, bacteremia, endocarditis and meningitis with this partnership.

In 2011, our economy flourished as the MRSA infection rates shot up with more than 80000 invasive infections, according to the human CDC or Centers for Disease Control and Prevention. Our accountants reported 11,285 MRSA related deaths in the same year, as was stated by CDC. Our close friends, the community of Neisseria gonorrhoeae (causing gonorrhea), are also resistant to penicillin. Our bacterial community has grown stronger with Mycobacterium tuberculosis (causing tuberculosis) extending their hand in resistance alliance, as they joined the bandwagon by being resistant to various drugs, and getting their new name: multiple-drug-resistant Mycobacterium tuberculosis (MDR-TB). Our numbers have exploded, our genes have mutated and the Resistance Movement is seeing a new dawn every 12 hours with each new generation. Although the humans are trying to synthesize new drugs and researching ways to control and defeat us, we must stay strong. We must show great spirit like Phyl Aureo the First. He may not be here with us, but he will always be alive through his genes in our cells.

Thank you.”

“Thank you for the amazing insight, sir. I request those who have registered for the Horizontal Gene Donation Campaign to stay back with their respective recipients.”

Written by: Ms. Sharvari Narendra (@DiabolicalDesi ) 
the first prize winner for the blog competition organized by 'The YSS Lab'.
Blog competition

BUGS BUDDIES!! (2nd Prize winner: Blog competition)

They are invisible to us. But believe me they are with us, chilling on our bodies. For each cell we have 10 times as many microbes making us a complex system harboring these guys. But don’t worry, there presence is important as without them it’s impossible for us to survive.

Main microbes are bacteria, viruses, fungi and parasites. Talking about bacteria, you can’t escape them. They’re everywhere! Thankfully most of them doesn’t cause any disease and are useful to us. Taking an example, there are bacteria in our intestine that produces vitamins and allow them to be mixed in the blood. Just like this there are several evidences proving that these bugs on our bodies are our buddies rather than a foe. One should also note that these microscopic friends of ours can change there mind and make us ill (if they want :p). Such buddies are called as opportunistic pathogens, S. aureus being a perfect example of it.

Now we should look what makes them so important that we call these strange looking creatures our buddies. First and foremost, they make our food delicious. Yeast has been used since the time of Jesus to make bread. Some Lactobacillus species are used in pickling process as they enjoys the acidic environment. These bacteria are also used in making milk products like cheese and sour cream. Aspergillus produces the characteristic taste of soy sauce that we all enjoy in our Chinese dishes. Rhizobium is used in growing legumes. Bacteria are also used for curing meat.

Yeast S. cerevisiae is best known for brewing wine, beer and spirits along with bread making. Now who doesn’t want these! The process involves the mixing of sugar source with yeast and water. The ‘BT’ bacterium is used in killing pests and insects in farms due to its specificity and has established itself as farmer’s best friend over the years. Microbes are used in sewage treatment and are important part of denitrification process breaking complex organic matter. Microbes contribute to the field of medicine in the form of antibiotics. These are obtained from species like Bacillus and Penicillium. Streptomyces alone has more than 500 antibiotics in its arsenal. Ammonia oxidizing bacteria and archaea are used in aquariums to break down ammonia and prevent its build up. Ammonia enters the aquarium water in the form of fish waste. Bacteria can also be used in breakdown of biodegradable plastics. Heat tolerant bacteria, known as thermophiles are used in the process of composting to break down organic matter which in turn produces nutrient rich manure (with the aid of earthworms) used in farming. Complex communities residing on our bodies also maintains a healthy balance. There dis-balance can be problematic which gave rise to the concept of probiotics. Fecal bio-therapy also known as fecal transplant is also done to restore healthy balanced microbial community in the receiver.

Most of these examples may not look so important but these simple things promotes to an efficient living. Imagine what would be the consequences if they are not there?

Written by: Mr. Shahrukh Qureshi, Graphic Era University, Dehradun
(2nd Prize winner for the blogs competition conducted by 'The YSS Lab')
Blog competition

Microbial Chefs (3rd Prize winner: Blogs)

A foodie like me is always interested in all things related to food. I am very much fascinated by the word ‘chef’, no wonder after studying microbiology for five years I am happy to be labelled as a good chef.  I feel proud to serve spongy Idli and crispy Dosa, hot Jalebi and soft Dhokala to my family . I tell them I never go wrong in preparing all these delicacies as I am a microbiologist. Even in winter , when the temperature is not favorable my curd sets to optimum and tastes yummy…the reason, my microbial Chefs, they never go wrong, provided you give them optimum conditions.

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Lactic acid Bacteria: my favourite microbe ,sets my curd soft with that right taste of lactic acid .Now a days it is known as probiotic and is said to have Lactobacilli, Lactococcus, Leuconostoc and yeast.  These microbes enhance food digestion, produce useful products to destroy the bad microbes, complement the functions of the missed digestive enzymes (due to missed or defective genes), and to maintain the digestive system’s pH, and so on. These microbes after a long term consumption form a natural micro flora of our intestine. This prevents common problems of today’s world like hyper-acidity, constipation, loose motions, stomach upset, vomiting etc. one solution to  to all problems…My microbial chefs…and their products. So we should allow these chefs to take charge of our digestive system. These microbes must be producing some unknown nutrients which really bring you a sense of well being, satisfaction and comfort. The satisfaction it gives on a sunny afternoon..can’t be described. My humble request to the scientists or can I humbly throw it as a challenge is to please find out this Satisfaction Factor(SF) which these chiefs prepare for us so that by taking it as a medicine every one will become happy and satisfied.

Many people do not like curd and buttermilk but they do like Cheese which again is prepared by my microbial chefs. Different flavours, colors, textures and of course, taste is available in cheese. Rich in protein , yummy in taste, cheese also contain useful microbes. Cheese provides calcium and protein, as well as some vitamin A, B, riboflavin, zinc and phosphorus. It may have anti-cancer, weight-reducing, and heart-protective effects. Again my regular but fabulous chefs, Lactobacilli and Streptococci are responsible for making cheese. Propaianobacterium and Lactobacilli are the master chiefs  responsible for giving that peculiar flavour which is due to conversion of casein , a milk protein, to some specific amino acids (building blocks of proteins). Whatever may be its microbiology and biochemistry but all will agree that cheese tastes awesome …and it is healthy too.

With yummy cheese comes the name of pizza. The base of a pizza is made from white flour .This white flour is mixed with yeast available in market which produces acid and carbon dioxide due to fermentation of wet flour. Some times Leuconostoc and Lactic acid bacteria are also used. This gas makes the pizza crust chewy, light , airy and fluffy and spongy. All types of bread many bakery items are made using similar process. Now a days health conscious mothers like me make the pizza dough from roughly ground wheat flour and make a thing like pizza nutritious. Every one must appreciate the work of my microbial chefs here. No one can resist a piping  hot pizza.

To make spongy Idli and crispy porous dosa I just need to grind the ingredients well; my chefs are very particular ,they require it finely ground. Then add optimum amount of salt. What’s optimum, the one that you like and provide a cosy place .If it is cold outside keep in hot water or near your gas stove. The next day your Idli batter is ready. It is very much satisfactory for a cook to see the raised batter in early morning. It is like an exam result pass or fail; that tells me how my Idli is going to be.

My chefs not only are experts in making food but range of alcoholic beverages with variety of flavours is prepared by them. Lovers of seasoned old wine, will actually appreciate the art of these chefs. The process of storage and getting different flavours and aroma as time passes is interesting. This is due to variety of organic compounds produced by batches of these chefs.

Working in shifts and batches, handing over the product made by one shift to the next without thinking who will get the credit can only be done by microbes. But like us if many of them come together without minding the batch…they spoil the broth. Sometimes the curd becomes sticky ,sometimes it raises up with gases inside, sometimes it is too sour and sometimes it is not sour at all. By whose wish? off course my chefs and their masters that is you. Provide them good working condition and they will make wonderful food for you. I think temperature is the most crucial factor for my chefs. Any deviation from the optimal temperature and the chefs are angry, they die out, other chefs take the charge and cook in their own style. So  if you want it perfect provide perfect conditions.

My chefs can cook medicines for you that is ‘Antibiotic’ (Antibiotic is a self defense mechanism of microbes). Some genetically modified  chefs can make hormones like insulin for you. My chefs can sometimes cook something very fishy that is, they can even cook toxins in your food if you are careless. So how to get the work done from my chef depends up on you. Knowingly and unknowingly we all are coming across these little buddies, they give flavor, texture to  our food. If used tactfully can serve you wonderful food. Within very less time, with lot of hard work and  efforts they make different products like vitamins, useful acids, enhance digestion, improve overall health of a person. Microbial chefs can work miracles..only you need  to utilize them carefully and wisely.

 

Written by: Ms. Ashwini Pathak, DSK School, Pune.
(3rd prize winner of the blog competition conducted by The YSS Lab)

Environmental Microbiome

Life in extremes!!

We are surrounded by an environment where we interrelate with different forms of life. The environment we are living in is very convivial, as it provides us the very essential things to sustain. But have you ever thought of living in places where you encounter hostile/critical conditions, for instance, extremely high or low temperatures, scarce food & supply of oxygen?

Is it really imaginable for a life form to sustain in such extreme conditions? Earlier we never thought of existence of any forms of life in such extreme conditions, but with several scientific breakthroughs and progressions in Science & Technology, we have identified various microorganisms, which do exists in such extreme conditions, like polar regions, volcanic ponds, desert rocks or oceans.

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You must be discerning how a life can survive in such punitive conditions? How existence is possible at above 100°C or below 0°C? The answer is adaptability. All life processes are regulated by both biological and environmental indicators, which allow life to adapt. The thriving microorganisms (extremophiles) are very simple and flexible life forms. They can express a different metabolism to lessen the harmful effects of the climate. The biochemistry of such extremophiles is really very interesting and has revealed the uncommon properties of living cells that we usually do not come across. The extremophiles exist by alteration/mutation of biochemical reaction mechanisms, like the presence of cold shock and heat shock proteins, which help to withstand the extremely low and high temperatures. Unlike nucleic acids & proteins, lipids also play an important role to maintain the integrity of cell. Scientists suggest that low temperatures enhance the unsaturated lipid contents in the cells to make them suppler, therefore helping the organisms at sub-zero temperature. Also, some of the microorganisms have been found to have anti-freeze proteins, which do not let the formation of ice crystals in the cells, at below zero temperatures.

Similarly, some altered biomolecules (primarily proteins) and other cellular & sub-cellular adaptation mechanisms have been identified which allow bacteria/ fungi to survive in the extremely acidic or alkaline conditions, or extremes of pressure, salinity, or desiccation. The most adept life forms are the polyextremophiles, which can survive several extremes at once, for example thermoacidophiles thrive in water that is both exceedingly hot and acidic, such as in volcanic ponds.

These established archives prove that life knows no barrier & can exist in harshest environmental conditions. For this reason, scientists are aiming to get the bio signatures outside the planet Earth. Some recent scientific breakthroughs proves that the life may exist on other planets, like Mars.

Beyond extremophiles, another challenge is to understand how life began on Earth, because we don’t know that yet. If we took all the life on Earth and threw it on Mars, some things would still be alive two years later. The question is whether life could have ever begun on Mars? When we think about life beyond Earth, we usually think of life on a planet that’s like Earth because we know life can work with liquid oceans, nice temperatures, lots of oxygen, and a thick atmosphere. But by studying extremophiles, we find that life can survive in environments that are not good enough for us, but plenty good for them. The bottoms of oceans, temperatures above boiling points, very cold regions—all these are the kinds of environments we would find on lots of planets that might not be the place to build condos, but might be festooned with life.

Many questioned, what is the importance of knowing about extremophiles? How can it benefit the society? The answer can be ascertained from the advancement in Science & Technology, which has revealed many rare facts about life in the extremes. The extremophiles produces unique molecules to combat the stress conditions, which have been identified as likely sources for various novel compounds that can help in medicines & other industries like textiles, paper, synthetic chemistry etc.

We’re continually discovering new bizarre ecosystems on the face of the Earth and an entire extremophilic microbial world remains to be explored deep in the subsurface of the planet. As each of these ecosystems is scrutinized, we take one step closer to finding life on another world.

Written by: Dr. Kusum Dhakar (@The YSS Lab). Edited by: Sharvari Narendra
Human Microbiome

Poop- A pronounced Salvager

Yes, I can almost see the wrinkling of your nose the minute you read the title. But before you decide not to read the blog at all (because why would anybody want to read about feces), what if I tell you that your poop can save someone’s life? Your ‘bae’ (Danish word for poop) can save your ‘BAE’ (Before Anyone Else- that is- your loved one). Your trash, is quite literally, another man’s treasure. Before I get carried away with more metaphors, let me tell you what your doo-doo can actually do, and how.

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You may have heard about various kinds of transplantations- be it organs like heart, kidney, liver etc., or Dr. Batra’s very famous hair transplantation. Let me introduce you to a simple, bizarre, slightly gross, but low-cost, low-risk, highly effective method- Fecal Microbiota Transplantation (FMT). Scientifically, it is defined as, “the engraftment of microbiota from a healthy donor into a recipient resulting in the restoration of the normal gut microbial structure” (Borody and Khoruts, 2011). I bet that’s even more confusing than the term itself. Let me explain. The gut harbors various endless microbial symbionts (those who benefit themselves by using our resources and indirectly benefit us). The transplantation of these microbes in the form of feces, from a healthy donor to a patient who is suffering from some kind of intestinal disorder, is nothing but FMT.

Presentation4Image source: Dr Simon Goldenberg http://www.england.nhs.uk/wp-content/uploads/2015/04/10-cdi-practical-aspects-faecal-microbiota-transplant.pdf

The technique seems quite simple and interesting, but why should it concern you? There is one serious infection which affects the colon, called Clostridium difficile colitis, caused by Clostridium difficile. These bacteria overpopulate the colon when the good bacteria in the colon have been killed or suppressed by usage of antibiotics. Clostridium difficile colitis cause often debilitating, sometimes fatal diarrhea, and already CDC reports have shown that approximately 347,000 people in the US alone were diagnosed with this infection in 2012, of which at least 14,000 died. FMT is being widely used in the western world for treating this infection. It is also being recently used to treat inflammatory bowel disease, which includes ulcerative colitis and Crohn’s disease, and other gastrointestinal (GI) disorders such as the irritable bowel syndrome. Recent studies have also demonstrated the possible usage of FMT in treating obesity, metabolic syndrome and diabetes mellitus.

The use of feces as a therapy dates back to fourth-century China, where Ge Hong described its use for the treatment of a variety of conditions including diarrhea. Eiseman and colleagues, in 1958, introduced FMT into mainstream medicine, by describing the use of fecal enemas as a treatment for pseudomembranous colitis. It has gained popularity in the US in the past few years, although the total number of treatments to date in the US is less than 500 patients, according to experts, despite the success rate being above 90%.

Then why is India lagging behind in accepting FMT? I think it is probably due to the inherent ethics. Unlike FMT, probiotics generally do not stimulate the gut microbial community structure. Therefore, FMT can be a very effective option and solution for intestinal disorder treatment, especially considering the high prevalence of intestinal disorders in India. So, it is a high time that we use FMT in our clinical practices, as a potential therapeutic approach to treat dreadful GI tract diseases. This however demands efforts in creating awareness of this technique by making people understand the proven efficacy and benefits of this approach.

Let’s keep a goal of serving humanity.

Written by: Rakeshkumar Yadav and Sharvari Narendra

 

Environmental Microbiome

Lonar Lake: The key to understanding the process of life is gradually dying

If you have ever visited Buldhana district in the state of Maharashtra, India, you would have obviously visited the majestic and mysterious Lonar Lake, a famous tourist attraction. The Lonar crater, where the lake was formed, is hypothesized to be established by a meteorite impact, between 12000 years and 570000 years ago. This makes this body of water important for more than one reason. Culturally, it’s crucial owing to the Hemadpanthi temples surrounding it. However, from a geological point of view, it’s one of the only two craters in basalt rock (dark colored, fine-grained rock) in the country, and makes an excellent analogue for Martian craters (which is why Lonar Lake should be your next travel destination, unless you want to observe this wondrous phenomenon directly on Mars).

Lonar Lake

Here are some really interesting properties of the lake: the water in the lake is both hypersaline and hyperalkaline, meaning it has high salt content and high pH (the measure of acidity or alkalinity of a solution; seven being neutral). Thirty years ago, the pH here, was around 12. However, today, the pH level has dropped to around 10.5. The crater cavity is filled with breccias (a type of rock consisting of angular fragments of stone- incidentally, the type of rock also found on Mars). The lake is about 6 meters deep, and although there are several perennial freshwater springs and streams flowing into it, there seem to be no stream outlets from the lake.

These physicochemical properties of the Lonar Lake, in turn influence and shape the structure and function of the microbial communities which are found in this lake. Hence, the lake can support growth of unique lifeforms, such as microorganisms predominantly from the Firmicutes phylum, followed by Gammaproteobacteria, Actinobacteria, Alphaproteobacteria and Betaproteobacteria phyla. It’s no surprise then, that microbiologists have, for years, treated Lonar Lake, as an ‘area of interest’. It is an important source of microbial enzymes that can function at high pH, for example, alkaline proteases, lipases, amylases, chitinases, caseinases, etc.

Scientific research has certainly peaked, especially during the past decade. Besides my group from the National Centre for Cell Science, there is another team, from the Centre for Cellular and Molecular Biology in Hyderabad, which has been responsible for the discovery of several new bacteria at the lake. Experts are not interested in simply knowing the general nature of these life forms. They are also intrigued with the way these organisms survive and carry out their life processes at such extreme conditions. The outcome of such research is beneficial towards understanding the continuance of life in other hostile environments- probably even on other planets.

But the anthropogenic (human) activities occurring within and around Lonar Lake, over the past few years, are destroying this unique ecosystem. The dip in pH levels has been an obvious ominous outcome, but there are more signs. Construction and agricultural activities taking place in the vicinity of the lake, are taking a serious toll on this water body. Recent reports of a drop in the water level, owing to the digging of a bore well, were alarming in nature. There is some evidence which indicates that the source of water in the lake is actually deep under the ground. If that water is being drained by bore wells, the water supply to the lake would cease, causing the water levels to fall sharply, or, in the worst case, lead to the drying up of the lake.

There have been several efforts from concerned citizens, NGOs and researchers, to restrict destructive human activities around the lake. But these efforts have produced little success. There is now an urgent need to carry out a detailed study of the lake’s ecology and of the factors that influence it, followed by taking serious measures for its protection. The government could consider using the services of an independent authority- comprising experts from different fields- that has the full power to control development near the lake.

Without such measures, Lonar Lake could turn into a crater with some tourist cottages around it. If you want to know how that feels, ask Matt Damon.

Conceptualized by: Dr. Yogesh Shouche  Written and Edited by: Sharvari Narendra
Human Microbiome

Human Microbiome: Discovering your true inner self

Let’s do a small exercise. Leave all of your work and stand in front of a full length mirror, and take a good look at yourself. Then ask yourself the following question: “What am I made of?” Aside from flesh, bones, humanity, principles, morality, intelligence and all other adjectives that come into mind- dig a little deeper. What are you- a human being- made of? Cells. You are made of approximately 1013 cells. That number has zeroes which can’t fit in a calculator screen. But a bigger number, about 1014, is the number of organisms inside and on your body, Microorganisms. These diverse microbial communities, which are predominantly bacterial, are referred to as ‘Human Microbiome’. This number alone signifies the necessity of studying the human microbiome, and its importance in health and disease.

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Microbes are known to play a crucial role in human physiology and development, such as metabolizing indigestible carbohydrates and fats, producing essential vitamins, maintaining our immune systems, while also contributing 360 times more genes than our own genes. Extensive research has been carried out on the human microbiome, which shows that there are several factors, both intrinsic and extrinsic, such as genetics, dietary habits, age, geographic location, ethnicity, that contribute in molding and shaping the composition of the same. Increasing evidence suggests that this composition is essential, and any imbalance in this microbial composition (dysbiosis) can cause a wide variety of diseases, such as those ranging from neonatal health disorders, gastrointestinal disorders, rheumatoid arthritis, diseases associated with skin, lung, liver, urogenital tract, neurological disorders, cancer to lifestyle diseases like obesity and diabetes. It is because of this reason that many mega projects have been founded all over the world, for example, ‘The Human Microbiome Project’ (United States National Institute of Health), Australian Gut Project, British Gut Project, Initiative in Skin and Oral Microbiome (iMicroCare, China), etc.

Having established the fact that gut microbiota is associated with human health, let us take a look at another aspect. Assuming that you are still standing in front of the mirror, take a good look at your physical features. Now, imagine you are having dinner with Tom Cruise, Angelina Jolie, Shah Rukh Khan, Usain Bolt, Brett Lee, Jackie Chan, the Arabian Sheikh, and even though it is difficult to reach out, with the Eskimo. Aside from the fact that all of you are human beings, can you spot the differences between each of you? May it be hair colour, skin colour, height, body structure, shape of the face, eyes- and most importantly, diet. Each one of you is from a different place and your body is adapted to a particular diet. When there is different food present in each of your guts, you can hardly expect the microorganisms digesting this food to be the same. And because each population has a different diet, and different microbiome composition, it cannot be possible to generalize microbiome and disease association studies carried out in a particular population, with the other populations. This fact establishes the gravity and urgency of studying human microbiome in depth.

Having mentioned that, there is no denying the effect of gut microbial composition on human health. Let us consider an example, or more specifically, a hypothetical situation. For a few seconds, imagine yourself having the perfect body size and shape of your desire (since no one is ever really completely satisfied with the way they look). Now, look at your current situation in the mirror. This change in your body size and shape is associated with a change in the gut microbial composition. When people usually say the phrase “I have this gut feeling”, or “do what your gut tells you”, they aren’t lying. Gut microbiome composition tells you that you don’t feel good, that you have diabetes or kidney stones or ulcerative colitis, that your obesity is linked to its composition and that you should do regular exercise to change that composition (decrease the number of predominant microorganisms present in your unhealthy state), and literally watch your tongue (keep your diet in check). Studies on obese individuals and on surgically treated obese individuals have actually shown a decrease in the predominance of microorganisms from the Bacteroides genus and reduction in the archaeal population. These observations provide evidence of the association between gut microbial composition and various diseases, while also paving ways for ideas for treatment.

Additionally, did you know that maternal and child health is also associated with the human microbiome? What nourishment you get as a child is very important in shaping the gut microbial composition, keeping it in balance and consequently ensuring that you have a strong immunity, therefore resulting in proper development and growth as a child. If you compare gut microbiome composition of nourished and malnourished children, you will find that there are a higher number of beneficial microorganisms in nourished children. They have functions of producing enzymes (such as Carbohydrate-Active enzymes), which are necessary to generate energy from complex carbohydrates. And that’s not all. Gut bacterial community is shown to be associated with iron deficiency, tripartite association, intestinal function, and arginine metabolism in women. So the next time your hemoglobin is lower than average, ladies, kindly check if you are eating right. You would be surprised to know that early exposures such as breastfeeding and vaginal contact during birth (which would depend on whether you were a normal or a cesarean baby), are also very important in shaping and modulating the microbiome composition in infants, and therefore helping them in developing their immune systems.

The rising and leading probiotics (beneficial gut bacteria) industries such as Amul, Nestle India, Mother Dairy, Danone and Yakult, formed on the basis of the knowledge that maintaining the appropriate balance of microbes in the gut (in other words, avoiding dysbiosis) can thwart infection, employ organisms like lactobacilli and bifidobacteria, in developing a range of probiotic products, such as yoghurt, curd and several dietary supplements. Therefore, it can be seen that certain gut microorganisms act as palliatives for stomach upsets. In addition to that, gut microbes are also playing important and upcoming roles in the antibiotics industry. Vedanta Biosciences in Boston, Massachusetts, now acquired by Pfizer Inc, is conducting preclinical trials of a pill containing microbes that suppress gut inflammation.

Therefore, one can see how crucial it is to study human microbiome. Maybe the answer to living a healthy life has always been within us. Maybe, if we discover our inner selves, we can take a step closer towards finding remedies for all our problems. Microbiome research has a lot of potential, and it is about time we tap that potential, and uncover what we are truly made of, in order to understand what makes us who we are.

Conceptualized by: Dr. Yogesh Shouche and Mr. Shreyas Kumbhare (The YSS lab); Written and edited by: Sharvari Narendra

 

 

Uncategorized

It’s all about microbes: Microb(e)logging

What is the first thing that comes into mind when you hear the word “microorganisms”? You can literally hear someone in the background, screaming, “Kitanu!”

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“Kitanu” (Germs), the macroscopic (deliberately refered here as macroscopic) living beings one can see through iPads, by zooming in on the skin of a little boy, who has just come home from playing football, and is sweaty and dirty. The organisms, that soap brands guarantee a 99.9% safety against.

So what happens to the 0.1% organisms? These 0.1% bravehearts live to tell the tale of how there are a lot of misconceptions regarding microorganisms in general.

For example, microorganism, by definition, means that it is too small to be seen by the unaided eye. So unless these iPads, that the doctors in the advertisements possess, have secret microscopes installed in them, which are lightweight and technologically advanced and revolutionary, microorganisms cannot be seen by the naked eye.

And not all of them are harmful. The idlis and dosas that you devour every Sunday are actually fermented, or in simple terms, processed, by the activity of microorganisms. Not just that- we have over 100 trillion microbes both inside and on our bodies- and most of them are essential for crucial, quotidian processes, like digesting those idlis and dosas, or pizzas and green vegetables. In fact, we are more microorganisms and less human beings ourselves.

So what are these concepts and misconceptions about microorganisms? Why do people study these organisms and do extensive research on them for years? Is it just to look important in those white labcoats and take pride in being doctors? Or is it to implement and use this research in developing many therapeutics to improve the health of all living beings, and also to keep the environment safe?

This blog is dedicated to create awareness about microbial science in people, by translating the scientific knowledge into layman terms. “It’s all about microbes” is going to cover a myriad of topics, ranging from the basics of human microbiome, or the basics of microorganisms in human beings, to any Indian’s favourite topic- food, here, specifically, Indian fermented food. The blog will also be covering other important topics, namely, the hypothesis about hygiene, probiotics, lifestyle associated diseases, abuse of antibiotics, maternal and early stage healthcare, diet, biodegradation in cleaning the environment, and water resources and our responsibility in keeping them clean.

The best part about this blog is that it is written and conceptualised by researchers and clinicians all over India, from big and renowned institutes like NCCS, who have been working extensively in this field since years, and ergo, they know what they are writing about, and you can trust their word. If 9 out of 10 dentists recommend a particular brand of toothpaste, you can be rest assured that 10 out of 10 scientists would recommend you to read this blog. Do keep in mind here that these are actual scientists, which emphasises the authenticity of this blog.

So are you a hygiene freak who carries a sanitizer everywhere? Are you an amateur cook trying to get the idli batter to leaven correctly, or a gourmet interested in what is involved in the process of making your favourite food items? Are you concerned that your westernised lifestyle might be affecting your health, like those acnes you hide with a concealer? Are you a hesitant consumer of probiotics, wondering if the actors and actresses in the advertisements actually take them to remain healthy? Or are you just a responsible citizen, wishing that the river in your city could magically clean itself?

Whether you are a new mother trying to lose those extra Kilos, or a pregnant woman eating chocolate probiotic icecream- grab your husbands, your brothers and sisters, your friends, your parents, your nieces and nephews, your colleagues, and even your previous dieticians whose diet charts you didn’t follow- and read our blog “It’s all about microbes”, from a new and different perspective.
A perspective which will make a difference in your life.
So Ready (your devices)! Set (the brightness level)! Go (to our blog)! And Read!
Happy Microblogging!
Concept: The YSS Lab
Written and edited by: Sharvari Narendra
Essay competition

Microbes: the superheroes (1st Prize winner: Essay competition)

The word superheroes reminds us of our childhood cartoons or comic strip such as Batman, Superman etc. Who are endowed with superhuman powers and usually are portrayed as fighting crime, protecting the public and usually battling super villain. They are masked fighters working for betterment of mankind. All these are fictional characters and are only meant for entertainment purpose, but to our surprise there is someone in this world who is a real invisible superhero ready to work for you at your disposal and make your life easier. They are the “Microbes ”. Though Microbes are too small to see with the naked eyes, they have the abilities that put superheroes to shame.

The Bacteria are often thought of as harmful in day-to-day life as they are usually associated with the diseases that afflicts us. However,there exists a plethora of bacteria which are highly beneficial and crucial to the existence of mankind. Because of the presence of Microbes in all walks of human life, there is a constant interaction of the Microbes on human life. Most of the products we use on daily basis are of microbial origins. Bread, cheese, yogurt, curd, beer, wine, antibiotics, fossil fuels like diesel and petrol are some of the useful and important products synthesized by the bacteria’s. The word bacteria is generally coupled with a negative connotation due to lack of scientific knowledge or false beliefs. You will find them on your own body,both inside and out. In fact, we cannot live without them. Without Microbes the earth would be filled with corpses. They are vital participants of the food chain. Bacteria breakdown dead organisms, animal waste and plant litter to obtain nutrients. But they don’t just eat nature’s waste, they recycle it. The process of decomposition releases chemicals such as carbon, nitrogen etc which can be used to build new plants and animals. So next time you see cut flowers decay or vegetables rot, remember you are really seeing Microbes at work. They are nature’s scavengers.

Microbes are a key component in both home and industrial food preparation. Lactic acid bacteria are used to make yogurt, cheese, buttermilk and other fermented milk products. Yeast is used in manufacturing of beer and wine and for the leavening of breads. The Microbes keep us healthy. The Microbes that normally live in association with humans on the various surfaces of body called as normal flora which protects from infection. Your gastrointestinal tract is not your own but it is a big universe of micro organisms helping us to digest our food, it has now been established that metabolism of an individual is directly related to the type of gut flora present in their system.

Microbes also have medical and pharmaceutical application. Microbes are a source of antibiotics and vaccine. Antibiotics are substances produced by microorganisms that kill or inhabitants others. Microbes in nature molds such as Penicillium and Bacillus produces antibiotics. Vaccines are substances derived from microorganisms and are used to immunize against diseases. The Microbes that are the cause of infectious disease are usually the ultimate source of vaccine such as BCG, tetanus, etc is all made from denatured bacteria.

Other metabolically talented microbes can metabolize metals,acid,salt,methane,or even radioactive waste.Thus they are routinely used in treatment of sewage cleaning of mines,and degradation of industrial chemical. We need energy to power our computers and to fuel our cars. The great fossil fuel on which our society is completely dependent is a result of combined actions of many microbes Degrading organic matter buried in deep layers of earth. Under anaerobic conditions,Microbes use all the dead remain of animal and planets for their energy production. This result in production of petrol and diesel.

Some microorganisms have specialized role biogas formation is one of such phenomenon. Thermophiles which are stable at high temperatures break down waste material to form biogas and also help in remediation of soil. Just above every decade there is an unintentional oil spill and microbes help in breakdown of these oil. Oil eating bacteria breakdown to recycle the oils. Chemical components thus helping in controlling pollution.

Understanding microbes genetic has enabled us to use microorganisms in genetic engineering technique such as gene cloning and has given numerous benefits to the biotechnological industry. protein from the recombinant technology can be used to produce machines, synthetic vaccine and other vital substances such as insulin for diabetic individual. Microbes help reduce atmospheric nitrogen and transform it into ammonia important for agriculture. Another example of benefits of microorganisms in agriculture is their use as biological pest control.

Overall microorganisms are vital for life on earth and are more than disease-causing agents . Few microorganisms are pathogenic, but many more has the important role in various ecological and industrial processes, maintaining human health and everyday new discoveries are made that show microorganisms are crucial for scientific advances to be made for the betterment of mankind .The list of applications mentioned above is just a small drop in the ocean of use of microbes. So next time when you hear the word Bacteria don’t be worried.Relax,sit back and think of them as your friendly invisible superheroes which are working at your disposal and making your life easier.

The saying “NOT ALL SUPERHEROES WEAR A CAPE” indeed holds true for these tiny creatures.

Written by: Ms. Manasi Vishal Rajput, Mar Ivanios Convent school, Pune.
(1st Prize winner of the Essay competition organized by 'The YSS Lab')
Essay competition

Microbes the superheroes (2nd prize winner: Essay competition)

Amongst the 8.7 million species of living organisms existing in our planet Earth, the very pioneers of life are micro-organisms. Being the tiniest yet perhaps the most interesting and amazing living form, learning more about them is a treat to those who seek in interest in science, more specifically the field of biology. Today we will take a journey through the world of micro-organisms and their wonderful being.

When we think about micro-organism, automatically tend to think of the disadvantages of the creature. Meanwhile, we forget about all the good that micro-organisms bring to our life. Let’s us just try to think for a second about how life would be without microbes. How would our life be without bread, cakes, cheese and all of the fermented food we eat? How would we have survived without antibiotics? Without the process of ‘Decomposition’ how would life be possible? Thus, we realize how dependent we are on microbes for accomplishment of even the most basic tasks in our day-to-day schedule.  Indeed, micro-organisms are superheroes in every possible sense. Why and how can we say so? Let’s find out!

Antibiotics are very important a medication to us now-a-days. The definition of antibiotics is as follows: ‘A medicine that inhibits the growth of or destroys micro-organisms.’ As stated above, these medicines kill or stop the growth of the disease-causing micro-organism. Streptomycin, Erythromycin, Tobramycin, Aureomycin and Chloromycin are some very useful antibiotics which are manufactured with the help of microbes. Penicillin, prepared by Alexander Fleming in 1929, continues to be one of the most useful inventions ever. These days a number of antibiotics are being produced from bacteria and fungi. Antibiotics are even mixed with the feed of livestock and poultry to check microbial infection in animals. They are also used to control many plant diseases. This way a micro-organism strongly stands to the first quality of a superhero and acts as a saviour for us.

The next quality of a superhero is to provide to people their basic necessities and privileges. The main and major medium of obtaining these necessities lies in Agriculture. Agriculture not only supplies goods for intake of food, but also are very important to the establishment and functioning of industries and therefore defines our economy both directly and indirectly. In this field of agriculture micro-organisms play a great role. Firstly comes the contribution of microbes to the supply of nitrogen to leguminous plants. We know how pulses  are extremely nutritional and that they contain lots of protein. Their production is possible only due to Rhizobium bacteria. Secondly, a very revolutionary and trending concept of waste management is Composting. A very important step for faster decomposition of organic waste for formation of compost is culture. This culture too is made by bacteria or fungi. Lastly, micro-organisms and plants are many-a-times in symbiotic relationship which benefits growth of either party.

Food is an extremely important element of all of our lives. Micro-organisms are also great as chefs and cook a lot for us. May it be preparation of yogurt, dosa, idli, bread or cheese, everything is prepared by our talented microbes. Let us take an example of curd. Curd is prepared from milk. The milk is kept open for some spat time, normally 12-15 hours, where the bacteria Lactobacillus acts upon it, giving out lactic acid. When the bacteria used for the process is yeast (for e.g., In making of bread), the process of ‘Fermentation’ discovered by Louis Pasteur in 1857 takes place. Even wine is prepared by microbes.

If we scrutinize the history of the world, we will observe the great part of micro-organisms in it. Although this sounds absurd at first, we realize its appropriateness when studied deeply. It will be observed that civilizations flourish only where the soil is fertile, and they go on flourishing so long as soil remains fertile. Abolition of Sindhi Ghati, Bablion, Hadappa, etc. civilizations are clear examples. And the soil remains fertile due to micro-organisms, because ‘Humus’ which defines the fertility of land, is obtained by decomposition of waste organic material, which is done by microbes in the first place. Even a large number of species are at the verge of finishing due infertility of soil which results in lack of food. As microbes affect soil fertility, they ultimately affect our entire living standard.

Except the list of advantages stated above, microbes are necessary in many other industries. Microbe ‘Escherichia Coli’ is present in our intestine to assist in digestion. Microbes are used to tan leather and retting of jute. They are also used to decrease pollution in the most effective way, by ‘Gobar gas’. It works under the principle of fermentation. The fermenting bacteria degrade cellulose level of the cow dung and releases inflammable gases mainly consisting of methane. This biogas supplies fuel and rich manure. Microbes are also consumed e.g., Chlorella, Camira (extracts are rich in iodine). Besides, Diatoms are used in making glass and porcelain. The uses of this wonderful organism are truly countless.

Will all these advantages in almost every possible field, microbes, in contrast to their size, continue to largely impact the world. From inside our intestine to in bio-gas manufacturing plants, they are found everywhere, ready to assist us whenever we need them. Their ability of killing other harmful organisms, even if indirectly, their contribution in the availability of food to us, our economic benefit thanks to them, and their occurrence everywhere  and wherever is possible which complements their assistance makes them an ideal superhero. Therefore we can conclude that micro-organisms are as beneficial as they can be harmful. Revolution in many industries concerning techniques can be made using micro-organisms. These organisms may lead us through a path to a brighter future. Recently, a research stated that the DNA of a certain micro-organism may help cure many severe diseases that are in today’s world extremely fatal. Ultimately, it is for sure that these tiny superheroes of ours, will continue to help us and impact the world amazingly forever.

Written by: Ms. Ira Uday Ghare, DSK School, pune
(2nd Prize winner of the essay competition conducted by The YSS Lab)

 

Essay competition

A day as a bacterium (3rd prize winner: Essay competition)

She then continued “have come here to fulfill any one of your wishes but the wish can work for twenty four hours”, wait let me tell you what happened from the start. It was my birth day. Unlike my other birthday I did not have party. I went to an orphanage and gave some gift. I also played with them. It was one of my best birthdays so far. When I was just about to go sleep, a ray of bright light flashed through my window. IT was a lady. She had wings, a stick with a star on its top, wearing costly jewelleries and a beautiful dress. Oh my god it was a fairy. I pinched myself to be sure. Ouch it hurt, yes it hurt. Yes I am in reality. The fairy sat down and said “I am a wish fairy, today I made many children happy. So I am here with a gift”. She paused, looked at my surprised face and then continued “I have come here to fulfill any one of your wishes but the wish can work for twenty four hours”. Well that’s a big question I thought.

 I remembered that in biology we had learned about bacteria. Then I said to the fairy, “I want to be a pathogenic bacterium for a day”. She surprised. She said to me, “that is unique! girls like you wish about being beautiful, or having something, but you asked to be a bacterium and that too a pathogenic one. WISH GRANTED”, she waved the fairy stick. She said, “Tomorrow when you wake up you will be a bacterium. Sleep well.”

The next day after I woke up I found myself in the world of microorganisms. Then I felt weird and I saw the reason behind it. I had a rod shaped body, a thin flagellum on my head, many hairs like structures on my hard capsule. I remembered that it is called pili. Then I looked around, saw that I was inside a human stomach, there were many microorganisms around me of many different shapes and sizes. Then I noticed that beside me a bacterium just like me was entering a cell. The bacterium looked towards me and said, ‘Enter in the cell fast.” the bacterium then continued. I observed it and fast went to the cell, used a chemical to break the cell membrane, entered into it, reached the cell’s DNA and mixed my own DNA with it and then got dissolved. After sometime the cell dried up.

Hmm, I thought, this is what I have to do. I again looked around. Suddenly many irregular shaped bodies entered the stomach. There were cries around me, “Enter the cell fast the WBCs are coming”. Just then I saw a WBC approaching me. I immediately broke the cell membrane and entered into it, went to the nucleus my DNA with the cells and finally got dissolved in it.

This is when I opened my eyes; I realized that I was studying in my room. I felt good now. I had my real body back. The fairy came again and asked me about how was my experience. I told her everything. She then asked me what did I learn, I replied that I learned about different cells, how the bacteria enter the cells, how short their life span was. I also learned that even being pathogenic bacteria is difficult as they always have threat from WBCs and many other antibiotics. She smiled at me. I thanked her.

Written by: Ms. Ankita Swain, DSK School, Pune
(3rd Prize winner of the Essay competition conducted by The YSS Lab)
Essay competition

Superbugs (3rd prize winner: Essay competition)

In our colloquial conversations, the word super arouses the feelings of power, something different, a miracle that can save the planet, be it the ‘kryptonian’, superman or the extraordinary powers of people termed as ‘superhumans’. But Superbugs aren’t the circus bugs lead by the ant ‘flick’ against the army of grasshoppers, Superbugs are real and they are something that we should be concerned about. But what exactly are superbugs? A superbug is defined as a micro-organism (mostly referring to bacteria) that is resistant to commonly used antibiotics. So that’s like a mouse that has plagued your house but is resistant to the mouse traps you have laid to have it caught. Now that’s a matter of concern isn’t it? But what makes these bugs so powerful? What is different in them? How have they come into existence? To understand this we must start from the rudimentary level, understand bacteria, think like a bacteria, imagine you as a bacteria! (Bacteria are of several types for the sake of this article, the term Bactria would refer to Heterotrophic Parasitic Bacteria)

Bacteria are classified into two main types:

  1. Gram positive Bacteria
  2. Gram negative Bacteria

Based on their ability to absorb and retain the dye crystal violet. They differ in Cell Wall structure (Gram Positive Bacteria have a thick monolayer while Gram Negative Bacteria have a thin triple layer), Cell Wall composition (concentration of lipids, peptidoglycan, Teichoic acid, responsiveness to triphenyl methane and sensitivity to Alkali’s as well as antibiotics like penicillin. It is due to these structural differences that Gram Negative Bacteria are fewer suspects able to antibiotics as compared to their counterparts.  Does this mean diseases caused by Gram Positive Bacteria aren’t a major concern? Surprisingly the answer is no! The aim of any organism with respect to the ecosystem is the survival of the species. The discovery of antibiotics plagued the bacteria, killing them like the black plague wiped Europe in the 14th century. Thus these bacteria have constantly evolved, evolved to survive the world, and these are today what we call Superbugs!

At this point I would ask you to imagine yourself to be bacteria, well-educated bacteria. Your species is on the verge of going extinct what would you do? Yes, Reproduce! Create more of your species but with certain differences so that you can’t be killed! Fortunately (for the bacteria) Mother Nature thought on similar lines and thus these bacteria kept evolving to maintain their population.

Humans oh humans, this one species that loves to disrupt natures Balance to satisfy their wants…. They developed more and more antibiotics and doctors administer them to patients for quick recovery despite the fact the patient’s immune system could have taken care of the situation. Antibiotics are frequently given to poultry animals to prevent bacterial diseases rather than as a cure. This has had one far reaching consequence, i.e. the development of aerators known as Superbugs.

Yes, it is humans who themselves have yet again put their own race in danger. It is the overuse of antibiotics that has caused several bacteria to become immune to commonly used antibiotics for example Enterobacteriaceae (CRE) is resistant to Carbapenem and Staphylococcus aureus (MRSA) is resistant to Methicillin, Pseudomonas aeruginosa And Acinetobacter are resistant to multiple drugs. Thus the problem regarding superbugs is one of utmost importance; new methods of dealing with these microscopic prokaryotes must be developed. How long can the same antibiotics work? How long will antibiotics as a branch itself be successful, what will happen if bacteria evolved enough to become resistant against all the known antibiotics?

Why is this, the need of the hour? To answer this we need to understand the process of Sexual reproduction in Bacteria.

  1. Conjugation: Exchange of genetic material by direct cell to cell contact
  2. Transformation: Cell free or naked DNA containing limited amounts of genetic information is picked up by a living cell
  3. Transduction: Gene transfer from one bacterium to another by the means of a bacteriophage

These methods at least Conjugation and Transformation are very fast methods of reproduction. While transaction does have a very wide reach.

Let us suppose the drug resistance capability of the bacteria is coded by the plasmid present in it. Then that part of the DNA strand can be transferred to several bacteria in a very short span of time with the above methods of exchange of chromatin material and these superbugs now do possess an actual threat to the human race.

What are Plasmids and how are they related?

Bacterial Cells may contain some extra chromosomal hereditary determinants which are either independent of bacterial chromosome or are integrated into it. They confer drug resistance, toxin producing ability etc. to the bacteria.

Thus it is high time we humans find solutions to the problem we create. With rising conflicts and advancements in biological weaponry, superbugs aren’t something you want the opposition to have. It is the need of the hour to change our ways, not only come up with a situation to remedy the current crisis but also investigate the causes of this scenario (e.g. Over-administration of Antibiotics by doctors ), and look for solutions so as to prevent such an crisis from reoccurring.

Written by: Mst. Ameya Patil, St. Mary's Junior College, Pune
(3rd Prize Winner of the Essay competition conducted by The YSS Lab)