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Our Hidden Allies : The Microbiome


What is Human Microbiome?

The human microbiome is the collection of microbes, including bacteria, fungi, and viruses, that live on and inside the human body. Yes, you heard it right. They are present on almost all of the external surfaces of our body. And we are not just ‘tolerating’ them, they are actually important and healthy for our normal physiological functioning!

Fun fact: A normal person has 10 time more microbial cells in/on their body than their own cells.

Immune defects in germ free mice.

This microbiome is so important that it has been observed that experimentally controlled ‘germ-free mice’, have severe immune system defects. These GF mice are the ones that live in a sterile environment and are free of all microorganisms. They are more susceptible to infections by certain bacterial, viral, and parasitic pathogens. They lack natural antibodies, have poorly developed lymphatic organs, reduced myelopoesis and many more things.

Types of microbes.

To begin with, we have to understand two types of microbes, COMMENSALS AND PATHOGENS.  Commensals are those type of microbes that reside with harmony on external surfaces of human body without causing any harm. Whereas, pathogens are the microbes that cause diseases.

All microbes are not scary.

It is to be kept in mind that the purpose of the article is not to claim that microbes aren’t harmful; when indeed many pathogens cause diseases. Basic hygiene is definitely necessary. However, with the increasing prevalence of germophobia, extensive use of disinfectants/sanitizers and scary statistics telling us how many microbes might be on our eyebrow etc. there arises a need for everyone to know and understand that, it is normal to coexist with microbes. Not just normal, rather necessary to lead a healthy life. 

If this article is able to serve a purpose, it would be to give a new and less discussed perspective about the commonality of microbes and how we as humans have never lived without them. It would be to explain how our physiology is integrated with our microbiome. How they are not some freeloaders, just living on us and sucking up our nutrition. They are significant participants in our metabolism, immunity, mental health, mood, dietary choices etc. We as a species have never been ‘just humans’. We have always lived with a microbiome on us. Or rather, evolution and natural selection ‘selected’ us to have maximum fitness with billions of microbial cells existing with us.

The next obvious question is, where exactly on our body do we find these microbial cells?

Microbiome is technically present on every surface in contact with the environment. The complete skin, upper respiratory tract, external ear canal, external eyes, gastrointestinal tract (a tube like cavity running from the mouth to the anus, which constitutes mouth, food pipe, intestines and rectum), genital regions etc.

This figure is adopted from Grice, E. A., & Segre, J. A. (2011). The skin microbiome. Nature reviews. Microbiology, 9(4), 244–253.

Some concepts related to microbiome:

  1. The microbiome is extremely dynamic. It changes throughout life, i.e. the number and species of the microbes change when our diet, geographical location, age etc change. It changes when we hit puberty and it also changes if we have pets at home.
This figure is taken from Sharon, G., Sampson, T. R., Geschwind, D. H., & Mazmanian, S. K. (2016). The Central Nervous System and the Gut Microbiome. Cell, 167(4), 915–932.
  • Every person has their own microbiome. Microbial composition is different from one person to another. Not all people have same kind of microbial community at a particular location of their body.
  • The location of a particular species of microbe on the body is also very specific. Let us say if a particular species of a microbe exists on a particular region of the body, for eg. skin, then it does not mean that the same microbe would be allowed to exist by the immune system on a different region of the body, such as in the blood or tissue.

Microbiome and obesity.

Sometimes, a person’s microbiome can also be a influence their obesity status.

For eg: Turnbaugh (2006) et. al. performed an interesting experiment where they took two batches of non-obese germ-free mice. One batch received microbiome transplantation from a non-obese normally grown mice, whereas the other batch of germ-free mice received microbiome transplant from obese normally grown mice.

They found is that, the germ-free mice exposed to microbial transplant from obese mice became obese in some time, whereas the germ free mice that received a transplant from normal/fit mice remained the same size.

Indicating a correlation between obesity and microbiome. However a definitive cause-effect relationship is yet to be established.

It has been seen that mice that are put on a diet, have an increase in the population of Bacteriodetes flora in their gut intestine, whereas, Firmicutes decrease in number.

Instances where microbiome directly help us

Below mentioned are some of many examples of how microbiome directly helps our body.

  1. In the intestine, the microbes release some factors, that influence our intestinal cells through specific signaling pathways to secrete some very necessary hormones.
  2. Lack of microbiome exposure during growing years can also lead to autoimmune disorders. Immune system develops a sense of self and non-self during early growth years of a person’s life. Hence, when a kid is growing up, exposure to these ‘common’ microbes is important for the immune system to develop a wider range of tolerance. This establishment of healthy tolerance of immune system by commensal bacteria also aids in protecting an individual from allergies.
  3. Commensal microbes induce secretion of specific chemicals (IL-18 and IL-22) in intestine, which contributes to anti-viral innate immunity.
  4. Commensal microbes respond to cues in environment by releasing specific compounds. One way or other, these compounds can be sensed by the nervous system. This system helps the brain in gaining real time information about the environment.
  5. Commensal microbes synthesize vitamin K and B12 for us.

BACTERIOTHERAPY: It refers to the use of bacteria for curing illness.

Kaitlin Hunter, who suffered from a severe and fatal colon infection cured herself by accepting a fecal transplant from her healthy mother. The fecal transplant was investigated to have healthy microbiome, which helped in fighting the infection.

In conclusion, there is a lot more that is still left to understand about the ways in which we as humans interact with microbes. Understanding this would aid the understanding of multiple diseases more clearly.

In the end, I would like to add a note that this article is written in a people-friendly way. If there is any Biology enthusiast who would like to read deeper into these topics and know exactly what molecule is secreted by which species of microbe to induce which signaling pathway; references are provided at the bottom of the article.


  • Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature reviews. Immunology9(5), 313–323.
  • Turnbaugh, P., Ley, R., Mahowald, M. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).
  • Ahern, Philip P., and Kevin J. Maloy. “Understanding Immune–Microbiota Interactions in the Intestine.” Immunology 159, no. 1 (2019): 4-14. Accessed April 13, 2024.
  • Fiebiger, U., Bereswill, S., & Heimesaat, M. M. (2016). Dissecting the Interplay Between Intestinal Microbiota and Host Immunity in Health and Disease: Lessons Learned from Germfree and Gnotobiotic Animal Models. European journal of microbiology & immunology6(4), 253–271.
  • Thaiss, C., Zmora, N., Levy, M. et al. The microbiome and innate immunity. Nature 535, 65–74 (2016).

Vatsala Pandey

Vatsala is currently a Master’s student in Biology at IISER-TVM. She aims to do a Ph.D. in Biology and become a scientist. She has always been amazed by the wonders of biology. That, coupled with her love for writing and the need in today’s society to bridge the gap between the common public and science, leads her to be a motivated science communicator. She has worked at several places and written many pieces as a science communicator where she converts complicated research into people-relevant articles. She is our go-to person for any biology article!

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