Since the first human-like creatures walked the earth, they have been adapting their behaviour and physical features to better suit their environments. But scientists are beginning to understand that our human genes can’t take credit for every adaptation that has occurred throughout history. More and more evidence, it seems, supports the idea that our microbes played a part in how we evolved. The ‘hologenome’ model of evolution, first introduced in 2008 by Israeli scientists, considers the combined genetic information from a host and its microbes as a single unit of evolution that changes in response to new environmental challenges.

Now Dr. Michael Shapira, a researcher at UC Berkeley (USA) has authored a scientific paper that cites increasing data in support of the hologenome concept. Most of the data come from insect species, whose shorter lifespans allow study of multiple generations in a shorter time frame. But Shapira notes that the ideas could equally apply to mammals, including humans. The most extensive microbiota of a mammal host is located in the gut, and Shapira says this particular microbiota could contribute to host adaptation in several ways.

First, says Shapira, there are many more genes in the gut microbiome than there are in the human genome, so this extensive collection of microbial genes could facilitate more rapid evolution. Second, the gut microbiome exchanges microbes with the surrounding environment in a constant give-and-take (through behaviours such as eating and social contact); this microbial transfer includes the exchange of genetic information that could prove handy for the host.

To take an example of an insect-microbe interaction with the potential to shape evolution: Japanese scientists in 2012 observed broad-headed stinkbugs that encountered an insecticide in their environment; these insects acquired an insecticide-degrading microbe from soil that helped them survive the exposure and live to produce the next generation. So a gut microbe that, at first, seemed to be just one among many in the insect’s gut turned out to have a crucial adaptive function when it came to a challenge in the stinkbug’s environment.

“In my mind, this is an example of the advantages of having a flexible pool of microbes,” said Shapira in a Berkeley News article. “That’s one way to achieve adaptation.”

In the recent paper, Shapira proposed the existence of a ‘core’ pool of microbes in the host’s gut, which may be determined by genes, and a ‘flexible’ pool that depends on aspects of a host’s environment. The establishment of some microorganisms in the gut, he says, probably depend on both genes and environment.

As they continually gather new data, Shapira and other scientists will modify the hologenome framework so it accounts for what they know about the wide variety of host-microbe and microbe-microbe interactions. Little by little, we are coming to a better understanding of the complex cooperative system that made us humans who we are.


Shapira M. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis. Trends in Ecology & Evolution. 2016. doi: