Sequence your microbiome!

Some months ago I paid 23andMe about a $100 to analyze a mouth swab of epithelial cell and report back information on my genetic makeup, ancestry, health risks, etc. I was particularly interested in the SNPs (single nucleotide polymorphisms) that correlate with more or less risk for things like heart disease, alzheimer’s, etc. (The FDA has recently shut down their releasing that information to new subscribers because they have decided it is an untested medical diagnostic procedure.)

I want now to mention another neat test you can purchase for ~$100, where you send in a swab of your poop, mouth , and skin and are sent back information on your microbiome, the genes of hundreds of microbial species (microbiota) that share your body with you. Michael Pollan, the guy who has written best selling food books (Omnivore’s Dilemma, etc.) has done an engaging piece on this. Some clips:

To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this “second genome,” as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.

Disorders in our internal ecosystem — a loss of diversity, say, or a proliferation of the “wrong” kind of microbes — may predispose us to obesity and a whole range of chronic diseases, as well as some infections. “Fecal transplants,” which involve installing a healthy person’s microbiota into a sick person’s gut, have been shown to effectively treat an antibiotic-resistant intestinal pathogen named C. difficile, which kills 14,000 Americans each year....[there is concern] about the damage that antibiotics, even in tiny doses, are doing to the microbiome — and particularly to our immune system and weight. “Farmers have been performing a great experiment for more than 60 years...by giving subtherapeutic doses of antibiotics to their animals to make them gain weight...the “Westernized microbiome” most of us now carry around is in fact an artifact of civilization”

...a pristine microbiome — of people who have had little or no contact with Westerners — features much greater biodiversity, including a number of species never before sequenced, and ... much higher levels of prevotella than is typically found in the Western gut....these vibrant, diverse and antibiotic-naïve microbiomes may play a role in Amerindians’ markedly lower rates of allergies, asthma, atopic disease and chronic conditions like Type 2 diabetes and cardiovascular disease.

The successful gardener has always known you don’t need to master the science of the soil, which is yet another hotbed of microbial fermentation, in order to nourish and nurture it. You just need to know what it likes to eat — basically, organic matter — and how, in a general way, to align your interests with the interests of the microbes and the plants. The gardener also discovers that, when pathogens or pests appear, chemical interventions “work,” that is, solve the immediate problem, but at a cost to the long-term health of the soil and the whole garden. The drive for absolute control leads to unanticipated forms of disorder.

This, it seems to me, is pretty much where we stand today with respect to our microbiomes — our teeming, quasi-wilderness. We don’t know a lot, but we probably know enough to begin taking better care of it. We have a pretty good idea of what it likes to eat, and what strong chemicals do to it. We know all we need to know, in other words, to begin, with modesty, to tend the unruly garden within.