Gut flora is mostly influenced by species, not diet

Do diet and other environmental factors largely influence microbial composition in the gut, or is this mostly determined by the species of the host?

This is a question that has supportive research on each side, but a new paper by Ochman et al. offers more clarity on the issue.

The authors chose great apes (and 2 humans) as their study subjects.  They obtained gut microbial samples and sequenced mitochondrial DNA of the hosts from fecal samples of eastern and western lowland gorillas, bonobos, 3 species of chimpanzees, and 1 human from Africa, and 1 human from the U.S.  The authors provided a map:

Of 18 different phyla, Firmicutes, Proteobacteria, and Bacteroidetes made up over 80% of the samples.  The investigators performed a phylogenetic analysis of each sample, which did not reveal dramatic group distinctions.  However at the species level is where significant diversity was observed.  Importantly, as the authors summarize:

The topological concordance between the species-level branching orders obtained for hosts and their microbiotae shows that over evolutionary timescales, host phylogeny is the overriding factor determining the microbial composition of the great ape gut microbiota. This recapitulation of the species relationships in the frequencies of the microbial constituents of their distal gut communities contrasts with previous notions that diet is the most important factor governing the grouping of gut microbiotae within primates.

So why does this result contrast with other research?  According to the authors, their sampling depth was improved over previous studies, which were unable to accurately gauge diversity and abundance of the microbial communities.  This was apparently a limitation of technology and cost prior to now.

These results also established that the microbial phylogenies of the 2 humans, even though on different continents, were most attributable to species and not location, diet, or other local factors.  They also found that apes of different species located in a similar area had differing phylogenies.  To better control for the possible effect from diet, they examined chloroplast sequences from each fecal sample (obviously limited to whatever they last consumed) and found no wide differences in diet except for one species.

The patterns that resulted from the phylogenetic analyses suggest that evolution of the physiologies in apes over time shape the microbial communities most.  It will be interesting to see if this holds true with further human studies.  And this isn’t to say that small differences in microbial species in the gut don’t have significant influences on health, but their relationships with diet and other factors are still rather elusive from what i’ve gathered.


Ochman H, Worobey M, Kuo C, Ndjango J, Peeters M, Hahn B, & Hugenholtz P (2010). Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities PLoS Biology.