The Gut Microbiome – Our Second Genome

Published 12/13/2013. Updated 3/9/2014. Updated 2/3/2016. Last updated 4/14/2016.

Correction added on 2/3/2016:
Until recently, it was thought that the uterus and placenta were germ-free to create a sterile environment keeping the developing baby safe from infections. But recent research has demonstrated that fetuses as young as one week have a complex collection of microbes living in their guts – and the placental microbes most closely resemble microbes living in the mothers’ mouths.
To learn more about this new finding, see Not Sterile, After All: The Placenta’s Microbiome. (Collins, 2014)



The long held view has been that our bodies consist of 10 trillion cells, the products of the 23,000 genes found in the human genome. Recent research into the composition and role of the human microbiota or microbiome has revealed that we are home to considerably more cells dwelling inside us, mostly in our guts.
 The GI tracts of babies in the womb are sterile. We pick up an important first dose of bacteria as we pass through the birth canal out into the world. Then we acquire additional bacteria from our nutritional intake, the environment and other humans via suckling, being caressed and kissed. At about a month after birth, the primary intestinal microflora of vaginally born infants has become well established.
 In contrast, the primary gut flora in babies born by C section may be out of balance for up to six months after birth. These babies do acquire some of their mothers’ microflora but their initial exposure is mostly from the environment (the air, nursing staff, other infants). Amazingly, as adults, we each have approximately 2-5 pounds of mutually beneficial tiny organisms living inside our guts – they help us while we provide them a cozy home.  (Wikipedia, 2013)                              



This collection of 100 trillion cells living inside us consists of several hundred species of non-human genes – at least 1,800 genera and up to 40,000 species of bacteria, together possessing 100 times the number of genes in the human genome. (Forsythe & Kunze, 2013) This vast amount of gut-dwelling organisms is not even manufactured by our own bodies! The majority of them are various bacteria, but there are also fungi, protozoa, viruses, yeasts and Archaea (single celled organisms characterized by their ability to tolerate extremes in temperature and acidity – Archaea are primitive life forms that appeared on earth billions of years ago but were only identified by scientists in the late 1970’s). (Wikipedia, 2013) (American Society for Microbiology, 2012)
And most shocking of all, it turns out we need these little aliens inside us and could not thrive – or even survive – without them. (Cryan & Dinan, 2012) (Forsythe & Kunze, 2013)
So, as a result of fairly recent advances in science,  we now are aware that humans are not really single organisms at all: We are actually complex eco-systems made up of a multitude of smaller, alien organisms working together among themselves and with our bodies to make us who we are. (Cryan & Dinan, 2012)


 To put this illustration another way, we are only about 10 percent human. Our other 90 percent is made up of microbial organisms. Not exactly how you’ve been viewing yourself, is it?
These alien components of our microbiomes interact with their hosts – us – to try to achieve a health-producing homeostasis. When the microbiota is diminished or unbalanced, deterioration in gastrointestinal, neuroendocrine or immune relationships take place, leading eventually to a disease state. (Cryan & O’Mahony, 2011)
The GI tract is an important hub of interaction between the body’s largest concentration of immune cells, a network of 500 million neurons in there, and the gut microbiota.
We know that the gut and brain communicate with each other via neural pathways as well as immune and endocrine mechanisms. The vagus nerve is also an important pathway for the bacteria in our guts for sending signals to our central nervous systems.  The exact ways the gut microbiome communicates with the brain are not fully know yet – possibly via a combination of neural, endocrine and immune pathways. (Cryan & Dinan, 2012) Researchers are understandably eager to solve the puzzle of what is sometimes called our second genome so they can develop microbial-based therapeutic strategies to correct mood disorders and any number of other health problems. (Forsythe & Kunze, 2013)

An Artist’s Vision of the Human Body with Its Microbiota
Credit: The Economist/Jon Berkeley
The topic of the gut microbiome is so new that many of the bacteria discovered in new research studies are still unnamed, without descriptions or sequenced genomes.  For some microbiome bacteria, scientists can’t even assign them to a specific bacterial genome. This is truly an exciting new frontier with vast implications … some of which I’ll talk about on other pages.



American Society for Microbiology. (2012). Microbe Beta World, Archaea. See

Collins,F. (2014). Not Sterile, After All: The Placenta’s Microbiome. See:

Cryan, J.F. & Dinan, T.G. (2012). Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13:10, 701-712.

Cryan, J.F. & O’Mahony, S.M. (2011). The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterology & Motility, 23:3, 187-192.

Forsythe, P. &  & Kunze, W.A. (2013).  Voices from within: gut microbes and the CNS, Cellular and Molecular Life Sciences, 70:1, 55-69.

Wikipedia. (November 16 2013). Gut Flora.  See


A version of this page content will appear in my forthcoming 2014 Oriental Medicine Journal article THE MICROBIOTA-GUT-BRAIN AXIS: The constant two-way communication between our guts and our brains.

© Copyright 2013-2014 Joan Rothchild Hardin. All Rights Reserved.

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19 thoughts on “The Gut Microbiome – Our Second Genome

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      Gut: The Inside Story of Our Body’s Most Underrated Organ,204,203,200_QL40_&dpSrc=srch


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