Chimpanzee microbiome variation is like ours

A new paper by Andrew Moeller and colleagues surveys the variation in species composition of gut microbiomes in the chimpanzees from Gombe, Tanzania Moeller:2012. They found that chimpanzees have a very similar pattern of variation to that found in human populations. Here's their mini-review of the human variation in "enterotypes":

The gut microbial communities in contemporary populations of humans have been partitioned into three clusters, termed enterotypes, each of which is characterized by a distinct set of overrepresented bacterial genera. Whereas initially no relationship was detected between enterotypes and specific features of the host (such as age, health status, body morphotype, provenance or gender), recent work has revealed associations between enterotype and long-term diet: the Bacteroides-dominant enterotype is prevalent in individuals whose diets are high in animal fat and protein, whereas the Prevotella-dominant enterotype prevails in individuals with high-carbohydrate diets.

A microbiome is a multispecies community, in which each kind of bacteria has its own distinctive metabolic role. The entire bacterial is made up of different proportions of each bacterial genus. The "enterotypes" discussed here are defined by variation in the proportions of different bacterial genera.

A visual depiction from the paper helps to show the three enterotypes in humans and chimpanzees. Each is characterized in a principal components plot, which reduces the proportions of dozens of bacterial types into two dimensions. This reduction is possible because the bacterial communities have covariance among species abundances -- when Dialister is common for example, Ruminococcus also tends to be common. The consistent association of some of the bacterial genera suggests that the community as a whole is regulated by the host gut and immune system factors.

Bacterial enterotypes, after Moeller et al 2012

Figure 1 from Moeller et al. 2012. Original caption: "(a) Assortment of gut microbial communities into enterotypes in chimpanzees and humans. Shown are BCA visualizations of enterotypes (coloured ellipses), as identified by PAM clustering, with black dots representing abundance distributions of bacterial genera from an individual host and numbered white rectangles marking the centre of each enterotype. Panel (right) showing human gut enterotypes modifed from Arumugam et al.1 Bacterial taxa uniquely overrepresented in the corresponding chimpanzee and human enterotypes are listed. (b) Relative abundances of the three bacterial taxa that are principally responsible for the separation of chimpanzee enterotypes. Shown are means, ranges and first and third quartiles. Colour coding of enterotypes follows that in (a)."

The chimpanzees have the same associations among bacterial species as humans, which suggests that the ecology within the chimpanzee gut is regulated by similar factors. The paper makes it clear that the bacterial communities of chimpanzees and humans, despite the consistent similarity of enterotypes, do differ in many ways. There are some bacterial species that are common in chimpanzees that are rare in humans, or that are overrepresented in one chimpanzee enterotype without being similarly represented in the human equivalent. The paper does not provide evidence that the chimpanzee and human microbiomes have remained static from our common ancestors. Instead, it shows that there may be ecological factors or feedbacks that keep the variability within a trimodal dynamic.

Another interesting aspect of the paper is that the bacterial enterotypes of chimpanzees are not stable within individuals. The authors examined the microbiomes in 2000, 2001, and 2008, finding that every individual changed from one enterotype to another during that period of time. The Gombe community did not change in a directional way, and no obvious factors explain the changes in enterotypes for individuals:

As observed in humans, there is no obvious association between chimpanzee enterotype and host genetics or geography. When sampled in 2000, the siblings, Sandi and Shelton, and their mother, Sparrow, each possessed different enterotypes, and their enterotypes changed, and still differed, in later samplings. Meanwhile, three chimpanzees that are not all members of the same family or same geographic community (Darbee, Gremlin and Kris) harboured the same enterotypes at each of the three time points sampled. In humans, diet is likely to be a major contributor to a hosts enterotype2. As the availability of different foodstuffs in Gombe can fluctuate seasonally15, 16, diet may also influence the possession of certain chimpanzee enterotypes. However, we found no consistent association between enterotype and the season in which a host was sampled. Furthermore, all three enterotypes were present during each wet season when foods were abundant and the diets among the chimpanzee hosts were the most homogenous.

All in all, I think this is a really fascinating study. The microbiome reveals something previously hidden, which may be important to dietary adaptations or immunity in hominoids generally. We might naturally assume that human microbiomes are products of very recent dietary innovations and rapid bacterial adaptation -- particularly among human agriculturalists. The chimpanzees may be showing that the important dynamics are much older than agriculture.