The Human Microbiome -- Eric R. Pianka

The Human Microbiome

© Eric R. Pianka

You are composed of about 100 trillion cells, but only 10 trillion are your own cells. Most of the other 90 trillion are bacteria, with a few other parasites, fungi, and nifty other little creatures, mixed in. The eyebrow mite Demodex folliculorum lives in your bushy eyebrow forests and burrows into eyebrow hair follicles (Buckman 2003) but causes little harm. Your health depends on many of these commensals. Some can cause cancers, others lead to allergies, asthma, diabetes, and obesity, and still others control appetite and enhance or inhibit immune function. Some of our contingent of microbes affect neurotransmitters and hence brain function as well as contribute to our moods and general sense of well being.

As many as ten thousand different species of bacteria exploit our bodies as favorable environmental substrates, one of the most important being the coliform human gut bacterium Escherichia coli, named for where they live: in our colons. Each of us houses 6 billion of these tiny commensal microbes, almost as many bacteria as there are people on planet Earth. They are not parasites but without them in our intestines, other less benevolent parasitic bacteria like Salmonella invade. When you lose your E. coli population, say by taking antibiotics, you get diarrhea. E. coli are vital to our well being because they keep our guts functional. Antibiotics can save lives but they also can also cause collateral damage by taking out beneficial gut bacteria. Indeed our good bacteria may well act as living antibiotics that protect us from harmful microbes. Many modern ailments, including allergies, diabetes, and obesity, are now thought to stem from incomplete microbiomes that have been reduced by antibiotics. When prescribing antibiotics, many doctors also recommend that patients take probiotics to replenish their intestinal microbiome. Yogurt sells because it acts in the same way. However, not enough is yet known to make specific predictions, let alone take action.

Of the thousands of bacterial species in our intestines, some, such as Helicobacter pylori, causes stomach ulcers and stomach and colon cancers in older people (Lampe 2008) but can also be beneficial at early ages. Children with H. pylori are much less likely to develop asthma than those who do not carry the bacterium. H. pylori also interacts with stomach hormones that influence appetite, and people without this bacterium are much more prone to overeating and obesity than those with H. pylori. However, as we age, this same bacterium can cause stomach ulcers and stomach cancers. Once, medical people wanted to eliminate H. pylori entirely whereas now the thinking is that its net effect is beneficial for young people but detrimental in adults. Ultimately, we may want to manage our microbiome populations in different ways as we age.

Before birth, babies live in a semi-sterile womb and have little or no microbiome -- during passage through a mother's birth canal, babies begin to acquire bacteria. Babies delivered by Caeserean section lack many microbes normally transferred from mother to child and are more likely to develop allergies and asthma than vaginally-birthed babies (Specter 2012). A friend of mine attributes his good teeth to his first kiss from his mother who inoculated his oral cavity with her own mouth's microorganisms. By the time a kid can crawl, he/she has been exposed to many trillion microbes, mostly bacteria, but also viruses and fungi (including yeasts). Although they are tiny, when added together, your 90 trillion cell microbiome weighs three pounds (as much as your brain!). Carrying around those extra three pounds is vital to your continued healthy existence.

Our microbiome commensals work constantly on our behalf, manufacturing vitamins, bolstering our immune systems, assisting in digestion, and preventing sinusitis and other infections. Bacteria even alter our brain chemistry thus affecting our moods and behavior. Some bacteria affect insulin resistance, others high blood pressure, irritable bowel syndrome, tooth decay, asthma and obesity.

A guy with a chronic ear infection once cured himself by simply transferring some earwax from his good ear to his bad one, presumably moving beneficial bacteria in the process (Specter 2012). A healthy person's sinuses harbor 1200 bacterial species, whereas someone with sinusitis has only 900 different strains. Those missing 300 species could be protecting against noxious microbes. All animals have their own unique microbiomes -- domesticated food animals fed antibiotics often gain weight just as people with diminished microbiomes become obese. Because of its implications for human health, the human microbiome has become the subject of intense study by the National Institute of Health. Interestingly, microbiomes of males differ from those in females (Bolnick et al. 2014). People can be classified into different enterotypes. This finding could lead to replacement treatments to restore missing bacteria and might even provide treatments for allergies, asthma, obesity, and tooth decay. The Human Microbiome Project has called for systematic fecal samples from many individuals to evaluate interindividual differences in gut microbial communities (Lampe 2008).

About ten percent of us harbor Clostridium difficile, which is normally held in check by other residents of the gut. When these companion bacteria are destroyed by antibiotics, C. difficile can erupt causing severe diarrhea and intestinal inflammatory disease. In extreme cases, destruction of the microbiome is so severe that doctors have had to resort to fecal transplants from healthy donors to re-innoculate the intestines of people whose microbiomes have become incomplete.

Darwin suggested the appendix, a pouch off the human large bowel, is a vestigial organ. When it becomes inflamed with a bacterial infection, appendicitis can be life threatening -- some surgeons remove the appendix as a normal proactive procedure whenever a patient's body cavity is opened up. Recently, however, Bollinger et al. (2007) have suggested the appendix could have an adaptive function serving as a "safe house" (a sort of "bomb shelter") for our commensal bacteria, facilitating recolonization of the colon by beneficial bacteria following exposure to antibiotics or pathogens.


Bollinger, R R, A S Barbas, E L Bush, S S Lin, and W Parker. 2007. Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology 249:826-831.

Bolnick, D I, L K Snowberg, P E Hirsch, L Christian, C L Lauber, E Org, B Parks, A J Lusis, R Knight, J G Caporaso, and R Svanba ̈ck. 2014. Individual diet has sex-dependent effects on vertebrate gut microbiota. Nature Communications |5:4500 | DOI: 10.1038/ncomms5500 | 1-13.

Buckman, R. 2003. Human Wildlife: The Life that Lives on Us: Johns Hopkins University Press.

Lampe, J W. 2008. The Human Microbiome Project: Getting to the Guts of the Matter in Cancer Epidemiology. Cancer Epidemiol Biomarkers Prev 17 (October 2008): 2523-2524.

Specter, M. 2012. Germs are Us: Bacteria make us sick. Do they also keep us alive? New Yorker (October 2012): 32-39.

Yong, E. 2016. I Contain multitudes. HarperCollins.

Last updated 7 August 2014 by Eric R. Pianka