Our Body is a Community (of bacteria)

Human Microbiome Spinler, J. 2013
Caption for Spinler, J. 2013  Types of bacteria in the human microbiome

We may very well be more microbe than human. Inside and on the surface of our bodies, we share space and nutrients with bacteria and viruses as well as other microbes. To be sure, our bodies are not overly hospitable to bacteria; our eyes have an enzyme called lysozyme which breaks open bacteria, killing them, while our stomach acid kills most of the bacteria we ingest. Our skin is salty, limiting its inhabitants to salt-tolerant microbes, and the bile in our small intestine represents another hurdle for bacteria seeking to survive and colonize our guts.

Nonetheless, to paraphrase Jurassic Park, bacteria find a way to survive in nearly every niche in our bodies–Helicobacter pyori lives in the face-meltingly acidic environment of our stomach (pH 1-3). Bacteria also regularly live in our eyes as well, despite the lysozyme; and certainly, pink eye is evidence bacteria can survive in the eye. Our guts are also full of bacteria, as evidenced by the current probiotics fad.

So what are these bacteria doing? Are they hitchhikers or nuisances or helpful? The answer, as it turns out, is it depends. Some are nuisances, with the potential to cause illness under the right circumstance. Others actively help us, and others are inadvertently helpful. For example, Staphylococcus aureus lives on the skin of about 1/3 of U.S. inhabitants. S. aureus can cause abscesses, cellulitis, scalded skin syndrome, toxic shock syndrome, and food poisoning. On the other end of the spectrum, Escherichia coli (non-pathogenic) is a normal inhabitant of our guts which makes vitamin K and B-vitamins. Additionally, some bacteria in the gut help digest complex carbohydrates and fibers that we can’t digest on our own (of course, this also has the byproduct of flatulence…).

Personally, though, I think the unintended consequences are the most interesting. See, the bacteria living in our gut also prevent foodborne illness. They accomplish this by several mechanisms–

  1. Essentially crowding out the newcomer pathogens. The normal bacteria will attach to the intestinal cell wall and prevent the pathogens from accessing it. Since many pathogens require access to the intestinal cells in order to cause illness, this can significantly slow down the pathogens.
  2. Reduce the amount of available nutrients. If there aren’t enough nutrients, the newcomer pathogens won’t be able to reproduce efficiently and will be more likely to be caught and disposed of by the immune system before they can reach the critical mass for causing illness.
  3. Make proteins which kill off competing pathogens. Pathogens can make these too, though.
  4. Make the environment less friendly for pathogens. For instance, the Lactobacillus bacteria in the vagina keep the pH low enough that it’s hostile to most other bacteria, including pathogens.

A lot of scientists are interested in how to tweak gut microbiomes right now, since this could provide better immunity as well as influence weight, anxiety, and even autoimmunity potentially. However, their research will probably not help the average person for a decade at least. So in the meantime, thank a microbe if you don’t easily get food poisoning.

Further reading:

General audience:

Mt. Sinai Healthcare–role of gut microbes in autoimmunity prevention: https://medicalxpress.com/news/2014-03-deeper-role-gut-microbes-immune.html

Nice NYT review of gut microbiome research.


Review of gut pathogen strategies; also covers role of gut microbiome (p3): https://ac.els-cdn.com/S1286457915000179/1-s2.0-S1286457915000179-main.pdf?_tid=ec1fcbc4-1793-4c3e-8d3d-ff4fae7b8720&acdnat=1535495136_6625d29640aa65d592561f8f58c9527a

Review of gut microbiome function in immunity. Abstract is straightforward/non-technical: https://ac.els-cdn.com/S1369527410001645/1-s2.0-S1369527410001645-main.pdf?_tid=4d87bbe4-b961-4afc-9a47-3dfe07953380&acdnat=1535495418_5fb0cab1ac227a547a590369cdac2a0b

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