Feces and phylogeny

A couple of weeks ago I wondered aloud about the question of whether diet-related changes in the nature of gut bacteria could have significant effects in evolution.  The paper I was writing about at the time showed that flies fed different diets quickly began to prefer mates who had been fed the same diet, and this preference appeared to be due to a change in the composition of gut bacteria.  But is the composition of gut bacteria maintained over evolutionary timescales? A recent paper (Ochman et al. 2010.  Evolutionary relationships of wild hominids recapitulated by gut microbial communities.  PLoS Biology doi:10.1371/journal.pbio.1000546) suggests that it is; but the role of diet remains unclear.

What Ochman et al. did was to collect the droppings (or fewmets) from 26 wild great apes, living in their normal habitats, and 2 humans.  What’s important here is that these were wild, untouched, free-living individuals (whom the authors in fact never saw); most previous studies of this kind had been done on animals living in zoos.  Ribosomal RNA sequencing was used to identify the microbial populations in the feces, and mitochondrial DNA and Y chromosome sequencing to identify the species and gender of the “donor”.  The authors then asked how different the microbial populations were between great ape species.

If you just look at the level of the bacterial phylum — Actinobacteria, Bacteroidetes, Firmicutes and so on — you see differences, but there is no easy mapping from bacterial phyla to ape species.  In other words, you can’t simply look for the signature of an rRNA from Proteobacteria and say, aha, that came from the gut of a gorilla.  But when you get down to the level of individual bacterial species, the spectrum of bacteria found in one great ape is markedly different from that found in another.  Even though there is significant variation from individual to individual — chimpanzee BB089 was particularly out there, carrying five phyla that were uncommon in all the other samples — it’s still possible to tell the difference between the great ape species just on the basis of the bacteria they harbor.  In fact, if you build a phylogenetic tree based only on information about the bacterial species in the feces, you get a tree that has identical topology to the “real” tree.  The different subspecies of chimps and gorillas, and humans and bonobos, are all clearly distinguishable and in their proper evolutionary relationships.

This appears to be strong evidence that we and our gut bacteria have indeed evolved together. This doesn’t quite address the original suggestion I was puzzling over, however, which was that changes in diet could drive changes in gut microbiota that would lead to speciation.  In fact, the great apes studied by Ochman et al. were living in widely separated parts of the African continent, and what they were eating therefore probably varied quite a lot.  The authors took a look at the diets of their “donors” by sequencing the chloroplasts recovered from the feces.  One shouldn’t put enormous weight on this, since it only tells you about what the individual ate in his/her most recent meals, but if you use the chloroplast information to make a phylogenetic tree you get nothing sensible.  In other words, there’s no evidence of a strong dietary preference from one great ape species to another, and thus no evidence (in the wild) of a strong dietary influence on microbiotal composition.

Diet aside, this is another piece of evidence that we need to start thinking of evolutionary selection as acting not solely on our own genetic variation, but on the (potentially enormous) variation of the bacteria we carry as well.  Very interesting.

Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, & Hugenholtz P (2010). Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS biology, 8 (11) PMID: 21103409