Is the microbiome part of the organism or part of the environment?

One of the central questions in the science of the microbiome is whether an animal’s genes or diet determine the composition of gut bacteria. This debate gets murky very quickly as it raises the fascinating question of whether you should consider your gut bacteria a part of you, just like the genes on your chromosomes in your gut cells, or a part of the environment that affects you, like a fruit that provides you nutrition on a daily basis or a parasite that occasionally makes you sick.

Approaches to studying gut bacteria in humans have largely been diet-centric, and we are reminded of this pattern by the news coverage this week of a heroic microbiome study by Rob Knight's and Jeff Gordon's labs. For starters, here's one good example published by Science Now - Your Inner Bugs are What You Eat. 

This study measured the number and types of gut bacteria in people from three very different populations - the Venezuelan Amazon, Malawian villages, and three American cities. Similarities and differences in their gut microbes were found but the news spin is that the microbial differences are driven by diet. This extrapolation goes too far, as these populations not only differ by diet, but also in so many other environmental and biological traits.

Diet clearly plays a role in shaping the microbiome. This fact is undeniable. But it is not the sole contributor. Genes are important and the relative importance of genes vs. diet remains a key question of the science of the gut microbiome. Before jumping too quickly into the diet camp, consider this observation.

• We raised insect species on exactly the same diets (download here), yielding a null hypothesis that if diet is the sole player in shaping the gut bacteria, then each species would have the same microbiome. To the contrary, evidence supports the alternative hypothesis that the microbial assemblages were different between the species and in fact the assemblages were related to each other in the same manner that the insects' genes were related to each other. To put it simply, even when diet is controlled for, the species' genes select for variation in the microbiome.

As in most scientific debates, it will likely be the merger of opposing ideas that ultimately fashions the knowledge. Diet and genes shape the microbiome. But whether your gut microbes should be considered part of the environment or part of you is up for continued discourse. What do you think?