Thursday, 6 November 2014

Even Our Gut Microbes Show Our Evolution From Apes

Picture: MicrobiologyBytes
Our gut bugs evolved with us as we split from chimps - health - 04 November 2014 - New Scientist

It's long been known that the evolution of obligate parasites such as lice and fleas closely parallels the evolution of their hosts, and now it seems the same parallels can be seen in the evolution of our microbiome - the ecosystem of gut bacteria and other micro-organisms that live in us and with which we have co-evolved and become co-dependent.

Basically, the 'friendly bacteria' that live in our guts not only aid our digestion by breaking down complex polysaccharides, etc, but they also keep our gut healthy by occupying niches, so excluding 'foreign' organisms. They also keep one another's populations in check so that none normally proliferates to levels which can be harmful. One of the causes of diarrhoea which often accompanies taking antibiotics is because the antibiotics can kill off some organisms so allowing others to proliferate.

Ochman and colleagues show that human evolution was accompanied by both a rapid divergence of the microbiome from the microbiome of apes, and a drastic loss of diversity of the microbial community.

Thomas Bosch,
Christian Albrechts University, Kiel, Germany
A team led by Howard Ochman of the University of Austin, Texas, USA sequenced the genome of the microbiome of hundreds of chimpanzees, bonobos and gorillas as well as hundreds of humans from US cities, Venezuela and Malawi. They found that the degree of divergence exactly matched the degree of divergence between the genomes of humans and the other anthropoid apes, with gorillas being more distantly related to human that chimpanzees and bonobos.

They also found that humans lost microbial diversity late in our evolution, probably as we changed our diet, eating more meat and less vegetation.

Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.

This loss of diversity, especially of those bacteria which help us digest plant materials, may have had had unfortunate consequences in that undigested complex polysaccharides may cause intestinal inflammation, for example, colitis. Loss of diversity also leads to loss of resilience. It could be that the advantages we gained from meat eating, and maybe from cooking our food, had a downside in this loss of biodiversity and its consequences, in an interesting example of adaptive evolution often being a balancing act between advantage and disadvantage with something quite small tipping it one way or the other.

The new study demonstrates that divergence of humans from great apes was accompanied by the establishment of a completely different, human-specific microbiome. Whether this change of the microbiome was one of the key drivers of human evolution and the development of human specific features remains to be shown.

Thomas Bosch,
Christian Albrechts University, Kiel, Germany
But a recent discovery in insects, where is was shown that differences is their biomes can prevent individuals of the same species from interbreeding, raise the possibility that we may actually be looking at this from the wrong direction when we assume it was human evolution and divergence from the other apes which drove the change in our microbiome. The discover in insects raises the possibility that our evolving and diversifying gut microbiome could have driven human evolution.

But should we be surprised by this? Should we not expect co-evolution leading to mutualism to be driven by either or both of the components? Evolving genes have no concern for which set of genes they happen to be in alliance with at the time nor that they should occupy the same nucleus of the same cells. If it produces more copies in the combined genepool in future generations then whatever produces that will come to predominate. There is no biological reason that it should be human, mammal, multicellular or even eukaryotic cell genes which drive coevolution towards mutualism. All it needs is 'selfish' genes.

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