“Nothing in biology makes sense except in the light of evolution.”

T. Dolzhansy (Russian Geneticist)

         “We admit that we are like apes, but we seldom realize that we are apes.”

                                             Richard Dawkins

human-ape_feetEvolution teaches us that humans and chimpanzees are “cousins”; both derived from a common ancestor in our past. We differ from chimpanzees in terms of our genetic makeup by only 4% (4% and not 2% as we previously thought). But in terms of our microbiome, our “second genome”, the differences are quite larger. A recent study of the microbiota composition of African apes – chimpanzees, bonobos and gorillas – indicated that the difference of their microbiome is 60-70% as compared to ours. Fossil and genetic data show that the separation of lineage of Homo sapiens from gorillas took place 8- 19 million year ago, while the separation from chimps and bonobos was in the range of 7-13 million years ago. During this evolutionary period the development of the primates’ microbiome diverged at a “clock-like rate”. On the other hand, scientists believe that the drastic divergence of human microbiome took place in an accelerated rate, probably only in the last hundreds of years.
Analysis of human microbiome across three continents shows that human gut flora is less diverse as compared to chimpanzees, bonobos and gorillas.  The biggest dissimilarity, 70% difference, was found with human populations in metropolitan areas in the US.
So, ancestral microbial diversity has been lost and we observe a major increase in groups of microorganisms that are associated with a diet rich in animal – based proteins and fat. When Homo sapiens were foragers and consumed a wide variety of plants, their diet contained abundant complex carbohydrates with a variety of chemical structures. This diversity in chemical composition enabled the maintenance of diverse microbial gut ecology. After the agricultural revolution, the loss in the variety of consumed plants -and in more recent decades, the use of antibiotics, births by C-sections and other lifestyle changes - caused dramatic changes in the human microbiome at a rapid pace.
This loss of our ancestral microbiome diversity and composition is probably linked to the occurrence of several chronic diseases. Loss of diversity (dysbiosis) has been shown to cause a compromised gut barrier (“leaky gut”) and consequently inflammation. This leads to autoimmune diseases, obesity, diabetes and other chronic ailments.
The 4% difference between our genome and the genetic fingerprints of our closest relative, the chimpanzee, is what gives us our distinct human traits. Our “second genome” is more amenable to changes. The composition of the microbiome, to some extent, can be modified through diet and lifestyle. This could slow down the spread of chronic diseases and alleviate some of their symptoms.   Reference: Howard Ochman et.al. Rapid changes in the gut microbiome during human evolution. Proc. Nat. Amer. Soc. 111, Nov 18 2014, 16431-5 Image credit: ‪www.halleethehomemaker.com