Last year I reviewed Ed Yong’s book I Contain Multitudes. After writing it I felt my review didn’t really do the topic justice. I joked that the microbiome is a bit like the Force from Star Wars. Besides a few uncanny functional parallels, what I really wanted to convey was that if we were to suddenly learn of the existence of a thing exactly like the Star Wars Force that was not fictional, it would be no more interesting or important than what we are currently learning about microbiomes.

In that spirit I started to jot down some ideas I had about stuff that might be interesting to think about in the context of microbiology. Some of these things may be common knowledge but I tried to think of interesting new ideas that were at least at one time attributed to even more mysterious causes. Coming up with creative ideas is an important part of scientific thinking and since some of these ideas are in the form of testable hypotheses, they are indeed genuine science. After reading this list, maybe you’ll think of some crazy ideas that we can call science.


  • It’s not just the trees in the forest that are important but I speculate that the forest floor’s health is probably as important. Related topics include fungi, deadwood, natural vs. managed forests.

  • House pets are an interesting new development. Though until recently humans often did live very close to livestock to keep them safe and to use them as a source of warmth. The 5th plague of Exodus is diseased livestock and the 6th is boils. Probably based on a true story.

  • Dogs. Rolling in stuff. Sniffing butts. Detecting cancer. Ya, they can.

  • Hypothyroidism in cats is weird.

  • Hotel rooms. Don’t watch this interview with hotel cleaning staff; one cleaner summarizes nicely: "Sleep in your car." My question is how do these intimate spaces shared by travellers distribute microbes?

  • Kissing and non-reproductive sex. Basically when the product of "inexplicably weird" and "stuff we enjoy" is quite high, look to the microbiome.

  • The microbiome of the birth canal is now recognized as an important thing. What about early skin-to-skin contact and breastfeeding for newborns? Maybe vernix interactions or umbilical subtleties. Discussed here. Related: how to design proper twin studies to eliminate microbiome confounds? Separate C-section from v-birth? Are there "genetic" links better explained by microbiome transfer.

  • Pregnant women eating dirt. Yup, they sometimes do that apparently. It’s called geophagia.

  • Things kids do, thumb sucking, licking stuff, eating dirt, boogers. Adults can almost be defined as humans who don’t like to think about that stuff but since the number one job of kids historically has been to not die of disease, I’m guessing subconscious kid habits are as evolutionarily optimized as anything.

  • Nail biting. Microbes love fingernails. Although articles like this jump to the conclusion that cooties are icky, the fact that nail biting is mostly subconscious and a habit that declines with age (as nails become harder and more brittle) makes me wonder if there is perhaps an immunological basis for fingernails. Also are long vs. short nails as a rough gender proxy producing evolutionary effects? And do painted nails affect things?

  • Animals licking wounds ("kiss to make better"). Oligopeptides found in saliva do seem to be complicated and interesting.

  • Deodorant, mouthwash, and other first world chemical hygiene products. Whatever you think they’re doing for you, it’s probably a lot more complicated.

  • Unnatural air conditioning, recirculation, HEPA filtering, household dust. Also complicated.

  • Spending an inordinate amount of life indoors. Or, same issue, reliability of lab animal models who live microbially isolated in sterile cages their whole lives.

  • Sleeping with mouth open vs. closed seems like an interesting difference if we assume the nasal passages are doing some useful filtering.

  • Sleeping itself — if not directly caused by microbes, they’re certainly counting on it now. What are the effects of poor sleep on critical microbiomes?

  • Dining al fresco is something all humans used to do but almost never do now. Seems like eating would be a good time to recalibrate microbes with the environment for better or worse.

  • Digging roots, shelling nuts, picking berries, handling food in a natural state. Forks were only introduced to Europe in the 16th century. In most of history people ate almost everything with their hands.

  • It’s easy to imagine that drugs that subtly interact with the microbiome could lose (or gain) efficacy in the future (due to fast evolving microbes). What FDA implications are there for an "approved" drug that eventually becomes useless? There may also be non-pharma folk remedies that may not work but may once have (or it’s complicated), like cranberry juice for urinary tract infections, cod liver oil, etc.

UPDATE 2020-03-11

You don’t have to read this article or the paper it’s writing about. Just check out the title and subtitle.

Bacteria in our guts break down dozens of popular drugs - Study suggests drugmakers should consider bacterial metabolism when designing and testing new drugs

  • Maybe old school poultices and chewed leaves really are effective wound therapy. (Though being a true king probably does not improve efficacy of chewed leaves as presented in the Lord of the Rings.)

  • Leeching, maybe not so crazy. Maybe it’s slightly better than nothing to grab any random swamp animal and let it interact with a very sick patient’s blood stream.

  • Perhaps the four bodily humors (black bile, yellow bile, phlegm, and blood) do control temperament. In all of known history the idea has only been ridiculous for around the last 100 years. With an increasing focus on microbes, it (or something similar) is getting less silly all the time.

  • As a serious athlete and back country hiker who lives in a desert, I know hydration can be the difference between life and death. However, I tend to find recommendations a bit excessive. (The CDC avoids official quotas.) I wonder to what extent microbiotas influence required water intake? What is the ideal way to modulate intake to recover from illness or microbial infection? Obviously dysentery, cholera, and other diseases cause water loss and show that these topics are not unrelated.

  • I’m a believer in the temperature effects of serious athletic activity. It is basically a controlled fever. What exactly those effects are is very difficult to say. Our species' (potential) athleticism could have evolved from persistence hunting or a microbe management strategy or both in parallel. Some people believe that cold is good. I have heard the speculative (testable) conjecture that cold water sports like surfing tend to produce fitter people per calorie burned than other types of exercise.

  • In addition to temperature effects, exercise in humans (and horses) may control skin microbes through mineral deposition.

  • The role of salt in the diet. Or, how salt started being used as an anti-microbial preservative in ancient times and affected our recent evolution.

  • As someone who lives near a beach that is regularly contaminated with dangerous bacteria I think the ocean’s salinity and mineral content are very interesting with respect to microbes and how they might have evolved and are still evolving. And beach sand. Let’s just say that I don’t do a lot of barefoot strolls on city beaches.

  • What is the importance of carrion birds in normalizing the world’s microbiomes? And birds of prey also eat carrion. Sometimes.

  • Some pooping in the lair/nest is tolerated by many animals. Birds build nests out of microbe managing tree parts.

  • Obviously radiation breaks atomic bonds that should not be broken in endogenous tissue, but how much of sun sensitivity is related to the microbiome’s tolerance for it?

  • What health effects can we predict from the microbial aspect of modern clothing, fur, leather, cotton, wool, foam bedding, upholstery, and related technology? Is polyester shag carpeting even more worthy of disgust than it seems?

  • The use of soap in laundry and bathing may be less important than the temperature of the water with respect to microbial activity. Obviously for modifying lipid polarity, soap is important by definition. The extent and nature of microbial interaction with such lipids is interesting.

  • What are the effects of clothesline drying in the fresh sunny air vs. baked in a dryer? Probably more than just evaporation.

  • What have the general microbial effects been of milk pasteurization, canned food, and other recent massively deployed food safety technologies? Food irradiation is interesting.

  • EMF effects on microbes? Mostly no it seems. Mostly.

  • Let’s rethink the hidden functionality of body parts that have been deprecated as expendable by modern humans, e.g. appendix, foreskin, gallbladder, tonsils, etc.

  • Besides saliva and sweat, it would not be shocking to discover extended microbial related functionality to menses, tears, urine, etc.

  • Burial vs. cremation (bury healthy corpses, burn sick ones?) A more radical idea: Could the urge for burial, i.e. an aversion to cremation, be a manifestation of a survival instinct of microbiota influencing human brains? Bear in mind our feline friends and Toxoplasmosis gondii.

UPDATE 2019-08-19

Scott Alexander has a very interesting article talking about exactly this kind of thing as he reviews this paper. The paper and Scott’s interpretation of it are interesting. It suggests that there are many complex parasites that modulate factors related to cognition causing "interesting" behavior in the hosts. Scott talks it up and then comes back down with some measure of skeptical realism. But he does concur that, right or wrong or somewhere in between, the premise is at least interesting.

  • Cramming workers into a cube farm or techbro mosh pit must surely have microbial consequences. I sometimes wonder if the modern office environment creates an intimate locale for microbiota that cause salarymen to all think alike.

  • Yawning. Though no one knows why we do it with certainty, I will add another hypothesis to the long list of suspects: microbe transfer. Unlike, say, the brain cooling hypothesis, the microbe transfer idea is coherent with the socially contagious aspects of yawning. Most likely there’s a combination of effects in play.

  • Conspecific fighting rituals are stupid. My hypothesis is that it is a way to spread the best microbes for an environment. The loser runs away with more of the victor’s microbes in his wounds. Again, combined with other important and complex effects.

  • Why do babies puke so much? Maybe the baby is giving the mom a chance to help selectively reinforce the developing immune system. Microbial activity could explain why pregnant women puke so much; I have no hypothesis for that though.

  • Microbe management could explain why a lot of animals, especially birds, feed their young vomit.

  • The system that causes vomiting (retroperistalsis) may have a role just moving gut microbes around even if actual vomiting is suppressed.

  • Traditional kooky food woo may have had some factual basis. Ironically halal and kosher probably suffer from literacy. Imagine some observant priests do some sensible causation correlation and give their tribe some weird food rules that turn out to be helpful. They thrive. But microbiomes evolve quickly. A tribe enjoying success with microbe management who are using written texts to lock their current practices into an unknown and changing future may not be doing themselves any long term favors.

  • Speaking of microbiomes evolving quickly — a key mechanism in our species' remarkable habitat adaptability — the entire premise of the paleo diet is idiotic.

  • Addiction. Seems there might be a link to various microbiotas.

UPDATE 2020-03-11

Today the Wikipedia page on alcoholic liver disease does not mention microbes. I expect that to change. This article called Bacteria Behind Yet Another Disease says the following.

"There have been mouse experiments that suggested that Enterococcus faecalis (a common human-associated bacterial species) might be involved in alcoholic hepatitis, but this latest work provides a great deal of proof that it might in fact be a causative agent. Presence of the bacteria in human stool is strongly correlated with [alcoholic liver disease]."

  • Microbes make me think of a new hypothesis for alcohol. Perhaps its pleasurable effects evolved to induce animals to eat rotten foods, picking up new microbes. Like flowers inducing bees to help.

  • Ingesting edible substances is one dimension, but what effects do their temperatures have on microbe health? For example hot or iced drinks? A "hot meal"? Also capsaicin spiciness hot, and acidity?

  • Cootie-phobe Michael Arrington believes that handshaking developed to show that you’ve got no weapon. I’m not so sure. Besides spreading pandemics and general disease, are there any redeeming features to this social technology? Could the custom be to slowly inoculate neighboring friendly tribes and vice versa?

  • I think microbiotas are starting to explain why getting "nutrition" in a pill (or drink) is much harder than people thought it would be. Sadly I predict that this is the fundamental limitation to spacefaring. Sorry Elon, I’m as disappointed about it as anyone.

  • Microbes are surprisingly similar to human cells — bacteria and yeast are commonly used as model organisms. How do toxins or even intentional metabolites affect microbes? For example, BPA mimics estrogen and millions of women take contraceptives or hormone replacement and then discharge it out into the environment. That one has been studied on ecosystems at a macro scale, but what about natural microbial environments? What about other metabolites?

  • Allergies and asthma.

  • Acne. It’s the same kind of mystery as asthma. Have we really evolved to be disfigured by zits? Seems so weird. And weird usually points to the world of microbiology.

  • Healthy human skin is a thriving forest of microbes carefully kept in balance by our bodies and what we do with them. Although some companies may be slightly aware of the microbiome’s role in healthy skin, it’s crazy to me how careless most cosmetics users seem to be about it. It also intrigues me that many traditional cosmetics and skin care treatments involve mud, vegetables, and other things that might be of interest to a microbe community.

  • Smoking is bad. But second-hand smoke may be disruptive to skin surface microbiomes. Here is a paper looking at connections between smoke and microbes. Here’s another.

  • What about second-hand antibiotics i.e. from the meat of livestock treated with antibiotics? This excellent microbiome article hints at it. For example, this article pretty clearly exposes meat eating as linked to obesity. I propose that latent antibiotics, not necessarily the meat per se, may cause havoc in conjunction with all the other trash modern people eat.

Here’s a microbiome wiki: MicrobeWiki

I’ll probably add to this list as I think of or come across interesting topics that fit the theme. If you see something that you think should be mentioned here, I’d love to hear it; send an email.

UPDATE 2018-05-18

My employer is doing some amazing work researching this topic. The American Gut Project is run from UCSD and has already produced some very interesting results. You can send in a sample and participate yourself!

UPDATE 2020-03-13