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Into the invisible: The Intriguing world of microbes


To solve the World’s biggest prob­lems, we have to look to the tini­est beings

From mak­ing the Earth suit­able for life by pro­duc­ing oxy­gen around 2.5 bil­lion years ago, to help­ing solve the unprece­dent­ed chal­lenges that mankind is fac­ing today, microbes play a much larg­er and more cru­cial role in the Earth’s ecosys­tem than we can com­pre­hend or imag­ine. They hold the key to under­stand­ing and solv­ing the most cru­cial issues right from soil fer­til­i­ty, to human health and water treat­ment. But where are these microbes? Every­where, lit­er­al­ly! There are tril­lions of these microor­gan­isms liv­ing right in your body.

Cyanobacteria or Blue Green Algae The first microbes on earth that could take CO2 and water and make sugars and the life sustaining Oxygen, through photosynthesis.

What is Microbiome?

We all know what microbes are. They include bac­te­ria, archaea, virus­es, fun­gi, and a vari­ety of oth­er micro­scop­ic life forms that are too small to be seen with the naked eye.

Micro­bio­me refers to the full col­lec­tion of genes of all the microbes in a com­mu­ni­ty. The human micro­bio­me includes all of our microbes’ genes and can be con­sid­ered a coun­ter­part to the human genome, which is all of our genes.

The Human Micro­bio­me

Micro­bio­mes lit­er­al­ly impact every aspect of our lives — the way we digest food, our immu­ni­ty, the weight we put on, our body odour, err..um.. mouth odour, and even our mood and men­tal health. We humans always like to draw bound­aries. We define our phys­i­cal space, the actions we do and the results of our actions. A small peek into the invis­i­ble world of microbes is enough to shake all the assump­tions we hold and all the achieve­ments we cred­it our­selves with.

Two people sitting next to each other share over 99.9% of their genes but only 10% of microbes. Personalized medicine and diet makes so much sense now!

What if you were told that you were more micro­bial than human? Its true! The microbes in our body out­num­ber the human cells. Not just that. The micro­bial genes out­num­ber our genes by 100 to 1. Each ecosys­tem on Earth is inhab­it­ed by dis­tinct and diverse set of species. The desert ecosys­tem is very dif­fer­ent from a rain­for­est. Sim­i­lar­ly, the micro­bio­me in each part of our body is very dif­fer­ent. The micro­bio­me in the gut, for exam­ple is very dif­fer­ent from the micro­bio­me in the armpit.

What deter­mines our micro­bio­me?

The moment we are born, microbes start col­o­niz­ing our body. Very young babies are cov­ered in a fair­ly uni­form mix­ture of microbes.


If a baby is born through the birth canal, a baby’s first microbes will pri­mar­i­ly come from his or her moth­er’s vagi­nal micro­bio­me. If new­born is deliv­ered by C‑section, instead of a micro­bio­me resem­bling the vagi­nal com­mu­ni­ty, the baby’s first microbes will look more like those found on the human skin.

Cae­sare­an births are also asso­ci­at­ed with high­er rates of a broad range of dis­eases, includ­ing asth­ma and food aller­gies. Their attri­bu­tion to microbes is an active area of research.

Our fam­i­ly mem­bers, envi­ron­ment and the food deter­mine the types of microbes that devel­op in the body. Babies giv­en breast milk tend to have very dif­fer­ent microbes than babies who are fed for­mu­la.

Friends or foes?

Well, both actu­al­ly. Friends, most­ly. They are essen­tial allies that help you live and func­tion, unless they are pathogens or start mul­ti­ply­ing in large num­bers in the wrong place.

Gut: The largest ecosystem of microbiota

There is a rea­son why your Gut is known as your sec­ond brain.

The largest, most impor­tant, diverse and com­plex micro­bio­me habi­tat is in your gut. With over 100 mil­lion neu­rons, com­plex neur­al net­works, sens­es and reflex­es, the sec­ond brain can con­trol gut behav­iour inde­pen­dent of the brain. Com­plex func­tions like diges­tion, absorp­tion of the nutri­ents, send­ing sig­nals across your body and rhyth­mic mus­cle con­trac­tion, all are done simul­ta­ne­ous­ly.

They also reg­u­late our metab­o­lism and deter­mine how much ener­gy we burn and how much fat we store. No two indi­vid­u­als have the same set of gut microbes. This could also explain why the same diet does not always work for two dif­fer­ent peo­ple. If they are not tak­en care of prop­er­ly and are dam­aged due to our diet or antibi­otics it may lead to dis­eases like colon can­cer, col­i­tis, dia­betes and obe­si­ty.

70 to 80 percent of your immune system is in your gut microbiome. This makes it so important to have a healthy microbial flora.

Many sci­en­tists point to the rise in dis­eases to the loss in key gut microbes. Today, our micro­bio­mes are far less diverse com­pared to micro­bio­mes of indige­nous peo­ple and pre­vi­ous gen­er­a­tions.

Recent research on the brain–gut–enteric micro­bio­ta axis has also estab­lished the impact of gut health on the individual’s emo­tions and mood by high­light­ing the inter­ac­tions of the gut micro­bio­ta with emo­tion­al and cog­ni­tive cen­ters of the brain. The Gov­ern­ment of India has recent­ly announced a 150 crore research project to study the gut of the Indi­an pop­u­la­tion.

The Antibi­ot­ic Atom bomb

Antibi­otics have an atom­ic reac­tion and wreak hav­oc. They can­not dif­fer­en­ti­ate between the ben­e­fi­cial bac­te­ria and the harm­ful bac­te­ria, and indis­crim­i­nate­ly kill both. Even a small dose of antibi­otics can cause sud­den shifts in the micro­bio­me and results in gut micro­bio­ta dys­bio­sis, i.e., dis­tur­bance in com­po­si­tion and func­tion. Though antibi­otics have helped save mil­lions of lives, they have long last­ing and far reach­ing neg­a­tive con­se­quences on our health sys­tem, and dis­rupt immu­ni­ty reg­u­la­tion and home­osta­sis.

Today, our human micro­bio­me is over exposed to antibi­otics, also due to their usage in farm ani­mals and crops. This alters many basic phys­i­o­log­i­cal equi­lib­ria, induces imme­di­ate risk for infec­tion and pro­motes long-term dis­ease.

How to devel­op a healthy gut micro­bio­me?

The aver­age lifes­pan of a bac­teri­um in your micro­bio­me is 20 min­utes. You can change your gut micro­bio­me with every meal you eat.

- Fer­ment­ed foods:

Fer­ment­ed foods like idlis and home made curds enhance the bio-avail­abil­i­ty of nutri­ents and are good for the gut micro­bio­me.

- Avoid processed foods and sug­ars

They get absorbed quick­ly into your small intes­tine with­out any help from your microbes. This leaves your gut microbes hun­gry so they begin snack­ing on the cells that line your intestines, caus­ing ‘Leaky Gut’.

- Pre­bi­otics and Pro­bi­otics

Pre­bi­otics are non-digestible parts of foods that feeds ben­e­fi­cial bac­te­ria colonies and helps to increase the num­ber of desir­able bac­te­ria in our diges­tive sys­tem.

Pro­bi­otics are live ben­e­fi­cial bac­te­ria that are nat­u­ral­ly cre­at­ed by the process of fer­men­ta­tion in foods like yogurt, etc.

The Earth

Microbes make up a major frac­tion of the bio­mass on earth and play a crit­i­cal role in the earth’s ecosys­tem, that sup­ports all larg­er organ­isms. They pro­duce much of the oxy­gen we breathe and are recruit­ed to clean up envi­ron­men­tal pol­lu­tion like oil spills or to treat our waste water.

Soil Health

Soils are thriv­ing hotspots for micro­bial diver­si­ty on Earth. The soil micro­bio­me pro­vide key life sup­port func­tions (LSF), which make life on Earth pos­si­ble:

  1. The pro­vi­sion of “fer­tile ground” as a basis for a sus­tain­able bio-econ­o­my, includ­ing the growth of food, feed, fibers, and bioen­er­gy crops;

  2. The main­te­nance of a nat­ur­al unthreat­ened plant bio­di­ver­si­ty at sites which are not used for agri­cul­tur­al pro­duc­tion;

  3. The safe­guard­ing of drink­ing water, by fil­ter­ing and degrad­ing pol­lu­tants in soil before they enter the ground­wa­ter body;

  4. The pro­tec­tion from ero­sion;

  5. The poten­tial to act as a sink for atmos­pher­ic CO2.

These tiny liv­ing organ­isms direct­ly con­tribute to the soil’s heath and bio­log­i­cal fer­til­i­ty. They are irre­place­able in the nutri­tion cycles- microbes are respon­si­ble for cycling many nutri­ents in our envi­ron­ment. They play an impor­tant role in the car­bon cycle. When dead leaves fall off of trees, who do you think decom­pos­es the leaves and releas­es nutri­ents back into the soil? Microbes. Microbes are also crit­i­cal to the nitro­gen cycle which allows plants to grow and pow­ers our farms. Bac­te­ria are the only organ­isms that can take nitro­gen from the air and con­vert it into a form that is usable by plants in the soil. Hav­ing these types of bac­te­ria in the soil means we need less fer­til­iz­er.

Nat­ur­al farm­ing

Con­ven­tion­al agri­cul­ture has a reduc­tion­ist approach to soil fer­til­i­ty. It is defined only by the chem­i­cal nutri­ents that it can sup­ply to the plants and its cor­re­spond­ing abil­i­ty to increase yield. This approach os using exces­sive use of chem­i­cal fer­til­iz­ers and pes­ti­cide on the soil has led to the death of essen­tial microbes in the soil ecosys­tem and even deser­ti­fi­ca­tion.

Nat­ur­al farm­ing pro­vides a holis­tic approach to soil fer­til­i­ty and takes into account its bio­log­i­cal diver­si­ty and its abil­i­ty to let soil organ­isms thrive. Cow based prod­ucts and using indige­nous for­mu­la­tions based on cow dung fer­men­ta­tion are com­mon­ly used in nat­ur­al farm­ing. Prepa­ra­tions such as ‘Pan­cha­gavya’ and ‘Jee­vam­rit’ are loaded with plant growth stim­u­la­tors and mil­lions of microbes.

Pad­ma Shri Sub­ash Palekar, pio­neer of Zero Bud­get Nat­ur­al Farm­ing (ZBNF) high­lights the impor­tance of cre­at­ing a con­ducive ecosys­tem for the soil microbes, by using cow based for­mu­la­tions. He also brings out the impor­tance of native cow breeds, which are supe­ri­or to for­eign cow breeds due to their diverse micro­bio­me. He says that the dung from the Bos indi­cus (humped cow) is most ben­e­fi­cial and has the high­est con­cen­tra­tions of micro-organ­isms as com­pared to Euro­pean cow breeds such as Hol­stein. The entire ZBNF method is cen­tred on the Indi­an cow, which his­tor­i­cal­ly has been part of Indi­an rur­al life, one gram of which con­tains 300 to 500 crore ben­e­fi­cial microbes.

Water qual­i­ty

Microbes also play an impor­tant role in clean­ing waste water. They can take organ­ic mate­r­i­al and chem­i­cals out of the water that would be tox­ic to humans, and use them to make oth­er non-tox­ic sub­stances, leav­ing the water clean­er than it began.

A lot of us have heard about the oil eat­ing bac­te­ria that we com­mon­ly use to try to clean up oil spills in oceans and oth­er bod­ies of water. Oil spills do a lot of dam­age to the envi­ron­ment but with­out these bac­te­ria they would do even more.

In our soils, the micro­bio­me is endan­gered by a vari­ety of fac­tors like cli­mate change, inten­sive chem­i­cal based agri­cul­ture, and extreme weath­er events. In our gut, we wreak hav­oc with the micro­bio­me by con­sum­ing processed foods and over expos­ing them to antibi­otics. Lifestyle, obses­sion with clean­ing agents and tox­ic chem­i­cals have even begun alter­ing the evo­lu­tion of human micro­bio­mes. But now we know why we should care.

If we think about it, microbes in every place act as invis­i­ble war­riors, tire­less­ly work­ing and main­tain­ing the state of dynam­ic bal­ance across earth sys­tems. Through mod­ern research, we have only begun to scratch the sur­face of the world of pos­si­bil­i­ties and solu­tions that micro­bio­mes have to offer. These are tru­ly beings that have been exist­ing before mankind, with mankind and will con­tin­ue to exist even after us.

References: Animated Life: Seeing the Invisible https://www.nytimes.com/2014/09/16/opinion/animated-life-seeing-the-invisible.html?smid=fb-share&_r=0 The Invisible Universe Of The Human Microbiome : https://www.youtube.com/watch?v=5DTrENdWvvM This animated documentary celebrates the 17th-century citizen scientist Antonie van Leeuwenhoek, whose discovery of microbes would change our view of the biological world.  Changing our diet influences the balance of microbes living in our guts. https://learn.genetics.utah.edu/content/microbiome/ecosystem/
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