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  • Writer's pictureJoan Rothchild Hardin

What’s in the Human Microbiome


Since I write about the human microbiome, I found this information on what’s been discovered – so far – about its interactions with the rest of the body quite fascinating and think you will too. The information is mostly from an article charmingly entitled Friends with social benefits – subtitled Host-microbe interactions as a driver of brain evolution and development?  (Stilling et al, 2014)

Our long evolutionary history has resulted in the modern human body’s being  home to trillions of colonizing microbes.


The microbiome is comprised of:


  •  Bacteria – at least 40,000 bacterial strains in 1,800 genera

  • Archaea (a group of single-celled organisms lacking a defined  nucleus) and eukaryotes (multi-celled organisms in which the genetic material is organized into a membrane-bound nucleus or nuclei),  such as  protozoa, fungi and nematodes

  • Many viruses, collectively termed the virome

The human microbiome collectively contains at least 9.9 million non-human genes. These non-human microbes carry about 500 times the number of human protein-coding genes that have been annotated to date.


In an adult human body, these approximately 100 trillion non-human associated cells weigh about 1-2 kg (2.2-4.4 lbs). Note: I’ve seen a variety of estimates for how much the microbiome weighs. When a weight range is given, I’m often not sure if it refers to the microbes living in the gut or to the microbes living in all the body’s microbiomes. Here’s a representation of the various microbiomes – there are others. Eg, different microbes live on various areas of our skin:


The average weight of the adult human microbiome is about the same as the average weight of an adult human brain – about 1.5 kg (3.3 lbs). Scientists think the comparable weights of our microbiomes and brains isn’t arbitrary but is instead “a window into the connections between neuroscience and microbiology. During human evolution, the primate brain underwent structural reconstructions of fast and dramatic increases in relative volume, leading to the brain as the most energy-demanding organ in the body.”


We’re still in the early stages of understanding how this symbiosis between the human microbiome and brain affects brain function and behavior. Stay tuned – this is a hot research area now. Microbes, RNA networks and brain development: A social triangle? An integrated model is proposed for the evolution of human social behavior.


Scientists have found evidence that the types of microbes in a given host influence a wide variety of physiological processes, such as post-natal development and immuno-modulation, as well as the host’s brain evolution and behavior.


The long-held belief that mammalian fetuses live in a sterile environment in the womb and first come in contact with bacteria during passage through the birth canal seems not to be true. There is increasing evidence that mothers transmit certain microbes to their babies in utero. “Moreover, the mother’s gut microbiota changes dramatically during pregnancy. After delivery through the birth canal, the microbiota becomes more complex and abundant, and these community-level changes continue via breast-feeding and uptake of new microbes from the environment. It is therefore not surprising that the microbiota critically influences pre-, peri- and postnatal development, and changes during early life stages will result in phenotypic alterations in adulthood.” (Stilling et al, 2014)


It is well-known that the composition of the microbiota changes during animal development and can be influenced by environmental factors such as diet, lifestyle, and habitat.


The hologenome theory of evolution posits:

  • Natural selection occurs because individual animals and plants act symbiotically with their microbial communities.

  • This casts the microbiome as a central player on a par with an organism’s inherited genes.

  • This relationship between genes and microbes affects both the host and its microbiota.

  • The interaction between the host’s genes and the considerably greater number of  genes in the host’s microbiota affects all aspects of the host’s life: development, survival, growth, adaptation, and reproduction. (Rosenberg & Zilber-Rosenberg, 2011)

  • The genetic information encoded by microbes is able to change, in response to environmental demands, more rapidly and by more processes, than the genetic information encoded by the host organism.

  • The mutated characteristics resulting from interactions between an organism’s genes and its microbiome are heritable from generation to generation.

  • “By all accounts, this viewpoint blurs the differences between the genome and environment. It embraces a vibrant and more satisfying view of the nature of biology, namely that the microbiome is as essential as the genome in defining what an animal or plant is and is not.” (Stilling et al, 2014)

Person + Microbiota


Lest you read any of this to mean that you’re doomed by either your genetic inheritance or the current sorry state of your gut microbes, I just want to point out that the composition of your gut microbiome can be changed by improving your diet and taking helpful supplements: ” … changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont (Note: = you + your microbiota) in the short term but also can be transmitted to offspring and lead to long lasting cooperations.” (Rosenberg & Zilber-Rosenberg, 2011)


REFERENCES Rosenberg, E. & Zilber-Rosenberg, I. (2011). Symbiosis and development: the hologenome concept. Birth Defects Research Part C: Embryo Today, 93:1, 56-66.  See: Stilling, R.M. et al. (2014). Friends with social benefits: host-microbe interactions as a driver of brain evolution and development? Frontiers in Cellular and Infection Microbiology. See: © Copyright 2015 Joan Rothchild Hardin. All Rights Reserved.

DISCLAIMER:  Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.

Comments submitted prior to 8/25/2021

Thanks for your clarification in advance. “The human microbiome collectively contains at least 9.9 million non-human genes.” Yet the circle graph (blue header) right above this quote shows the human microbiome to have only 1 million+ genes…….?


In reply to Neal

Neal, It is confusing. As I understand it, sometimes the comparison is stated as between the number of CELLS in the human body vs the human gut microbiome & sometimes it’s stated as between the number of GENES in those cells. Perhaps this will help:

I returned from three weeks in Iran just last night so am rather jet lagged & my focus is going to be out to lunch for at least a few days if not longer. If you manage to clear up this mystery, would you be willing to let me know what you’ve found? By the way, Iran is a fascinating place to visit.

Joan Hardin


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