The human microbiome has seen a huge boom in recent years, in terms of research, whilst in evolutionary terms the opposite may be true.
New research published in PNAS journal last week reveals that the human microbiome underwent a loss of gut microbial diversity after our ancestors split from chimpanzees and is specialized for meat-eating.
To understand how the human microbiome has changed over evolutionary time researchers investigated the gut bacteria of our closest relatives; the apes. Given that we shared a common ancestor, investigation of the gut microbiome of modern apes and the differences and similarities, if any, may help to shed light on our own evolution.
The gut microbiota of hundreds of wild African gorillas, chimpanzees and bonobos were sampled and compared to five different human populations spanning 3 continents, whose lifestyles range from hunter-gatherer to urban dweller.
Whilst the research data showed great differences between human and ape microbiomes they aren’t entirely dissimilar, with a number of common taxa shared between the different species, which could possibly represent the ancestral core of the African ape gut microbiome.
The study identified 35 instances in which the relative abundance of certain microbes shifted since modern apes diverged from a common ancestor between 8 and 19 million years ago and 17 instances which occurred in humans since the divergence of Homo and Pan (the genera of humans and modern common chimpanzees and bonobos, respectively)
These changes in the microbial makeup of the gut reflect not only the differing diets between humans, chimps and gorillas, but also have functional consequences for the host in terms of nutrition. Bacteroides, for example, which are associated with diets high in animal protein and fat have seen a fivefold increase in humans. Menthanobrevibactor, which helps to degrade complex plant polysaccharides has seen a fivefold reduction of their relative abundance in humans. Fibrobacter, a plant-fermenting bacterial genus common in the microbiomes of wild apes, has also been greatly reduced in humans.
Comparing Modern Humans
There’s been much news lately about the impact of our modern lifestyles and how they are taking their toll on our gut microbiota, from the use of antibiotics, chemicals like glyphosate and triclosan to cesarean sections and modern highly processed food, to name a few. To address this issue the research tied together gut data from a number of different sources to give a continent spanning representation of the modern human gut.
A 2012 paper revealed the differences between Amerindian tribes people of Venezuela, the people of rural Malawi and modern urban Americans (2). Into the mix they added data from the gut microbiome of the modern day hunter-gatherer Hadza people of Tanzania along with the data for 81 modern Europeans.
Modern urban citizens of the U.S. possess a markedly different microbiome, heavy in bacteroides whereas the Venezuelans and Malawians, for example, have a greater abundance of prevotella. Just what these differences mean in terms of health still has to be puzzled out, but compared to apes, humans have a greatly reduced diversity in their microbiomes, all in all, fewer phyla, classes, orders, families and genera regardless of the population studied.
What this means is that even though urban U.S. citizens have very different gut biota from rural Malawians or Venezuelan Amerindians, populations spanning different continents, inhabiting many different environments have a vastly reduced collection of gut microbes when compared to Pan and Gorilla. This goes a long way to confirming the idea that human microbiomes have decreased during our evolution. The alternative would be that the microbiomes of both gorillas and chimps have somehow greatly increased over the same timespan, which seems much less plausible.
Another way to look at this is to look at the beta diversity of samples taken. Beta diversity means the dissimilarity between communities of two samples or sites etc. The higher the beta diversity the more the two communities are dissimilar. One way of representing beta diversity is the Bray-Curtis dissimilarity index, shown in the figure below.
What we can see from the plot above is that even though the gut microbiota of U.S. citizens, Malawians and Venezuelans when compared side by side look quite different, when plotted against the ape data they are not so dissimilar, with the three human populations clustering together. The plot also shows the clustering of common chimps and bonobos and the markedly dissimilar microbiome of gorillas.
But what does this all actually mean? Well, it seems that as we evolved we lost a great deal of gut microbiota, primarily those associated with the degradation and digestion of fibrous plant material. The microbes that we kept, on the other hand, were bacteria that are associated with the digestion of animal protein and fats (amongst others). This idea gives further support to the hypothesis that we evolved on an animal rich diet.
Regardless of the make-up of the human diet, and how diets around the world vary in the present day, it seems that for much of our past animal products formed a big enough proportion of our diet to help shape the microbes that reside in our gut.
Now that certainly doesn’t mean that we evolved on meat, far from it, we are, as is so often forgotten; omnivores, and whilst all the pieces have yet to be put together it would seem that a combination of plant and animal foods would serve us better than a diet that excludes either.
Moeller AH, Li Y, Mpoudi Ngole E, Ahuka-Mundeke S, Lonsdorf EV, Pusey AE, Peeters M, Hahn BH, Ochman H. Rapid changes in the gut microbiome during human evolution. Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201419136. [Epub ahead of print] PubMed PMID: 25368157
Figures 1 and 2 are taken from the source paper, the biological classification diagram is sourced from Wikimedia commons