An Ecologist Ponders the Microbiome

Fluctuating nutrient concentrations and the timing of peristalsis may affect microbiome growth and composition, which is hypothesized to affect health. Certainly digestive upset is no fun for anyone, and it makes sense to look at inputs (diet) as the primary drivers.

Ecosystem arguments are used to claim that some forms of digestive upset are due to over- or under-growth of bacteria in the intestines.  For example, Small Intestine Bacterial Overgrowth (SIBO) is treated with what is called the GAPS diet, an effort to restrict all foods that bacteria can digest.

In response, Jeff Leach, of the American Gut Project, made this comparison between diets disturbing the microbiome and ecological disturbances:

"If you think about it from an ecosystem perspective or from an ecosystem restoration perspective, if you take any ecosystem like the gut, the microbiome, and if you starve it... If you starve your backyard and all the diversity of plants, if you just starve it of nutrients, all ships go down with lowering water. And that perturbation, if you will, it wouldn’t be on the same level as an antibiotic, but it is a perturbation; it is an insult. And when you insult an ecosystem, insults like fire, drought, nutrient overload or nutrient deprivation, any of these perturbations typically result in a flourishing of weedy species, in this case, opportunistic pathogens. I know the GAPS diet...from an ecosystem restoration standpoint, it makes absolutely no sense whatsoever to starve your gut microbiome at any level. "

This idea that "a healthy garden needs a healthy soil" is an ecological idea.  Jeff Leach goes on to claim that specific nutrients, like "resistant starch, non-starch polysaccharides like inulin and fructooligosaccharides and galactooligosaccharides, can provide food for the beneficial bacteria in your gut and can increase their levels by orders of magnitude."

Turns out it may be a false analogy, or if the analogy is valid, the hoped-for predictive power of diet on microbiome function may not hold up. While broad temperature-precipitation drivers do determine biome (e.g. tundra versus desert) it is almost impossible to predict the exact species in an ecosystem based on the nutrient inputs to that ecosystem.  And if microbiome bacteria exert their effects in a species-dependent fashion, it may not be possible to predict that eating x will cause bacteria xyz to grow.

Ecologists look (with envy, and skepticism) at nutrition research and commentary because we know how complicated ecosystems can mess with simplistic notions of cause-and-effect.