Into the invisible: The Intriguing world of microbes 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? Read about them

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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.

Image result for cyanobacteria

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, 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.


Animated Life: Seeing the Invisible

The Invisible Universe Of The Human Microbiome :

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.