There was a time when we thought the sum of the all the cells in our body, as mapped in our DNA, is what defines our living, breathing bodies. Then we discovered that inside us, mostly in our guts, live huge colonies of microbes, that are essential partners in keeping us alive and well. The mutually beneficial partnership is known as symbiosis.

And now scientists in the US reveal further astonishing evidence that runs contrary to current understanding. These microscopic fellow travellers, collectively known as the microbiome and unique to each species of plant and animal, also influence the evolution of host species.

In a July 18th issue of Science the researchers describe how by studying wasps, they found the microbiome has a similar effect to that of physical barriers like mountains and rivers in keeping species distinct and separate. They prevent any blurring of species distinction by killing off hybrids that arise when the males of one species cross with the females of another.

Seth Bordenstein, an evolutionary geneticist who heads a lab at Vanderbilt University in Nashville, Tennessee, and graduate student Robert Brucker, say their study supports the idea that the object of Darwin’s natural selection is not just the host organism but the host accompanied by its microbiome, a controversial theory known as the hologenomic theory of evolution.

The hologenome is the total genome of the symbiotic partnership of the host organism and its colonies of microscopic fellow travellers.

In a statement, Bordenstein, Associate Professor of Biological Sciences, says:

“Our research is focused on the question of who we are as humans? Who we are as animals?”

Describing their idea as “a high-risk proposition”, he explains there is an expectation among scientists that the origin of species is primarily governed by genetic changes in the nucleui of the organism’s cells, however:

Our study demonstrates that both the nuclear genome and the microbiome must be considered in a unified framework of speciation.”

Bordenstein says their findings shift the idea of hologenomic evolution from idea to observable reality, so that:

“The question is no longer whether the hologenome exists, but how common it is.”

He and Brucker found their evidence by studying three species of Nasonia, a genus of small match-head sized wasps also known as jewel wasps because of the emerald sheen of their bodies. Nasonia are a useful tool for biological control because they parasitize blowflies and fleshflies.

Brucker says Nasonia wasps carry a microbiome comprising 96 different groups of microbes. Two of the species they studied (N. giraulti and N. longicornis) are closely related genetically in that their evolutionary paths only diverged about 400,000 years ago.

He explains:

This closeness is also reflected in their microbiomes, which are quite similar. The third species (N. vitripennis), on the other hand, diverged about a million years ago so there are greater differences in both its genome and microbiome”,

When they tried to get the females and the males from the three species to mate with each other and make hybrid offspring, Bordenstein and Brucker found the vast majority, about 92%, of hybrid offspring from the two closely related species survived.

But hybrid offspring of parents from either of the closely related species mated with parents from the distant related species did not fare so well: over 90% of them died.

Brucker says when they looked at the microbiomes of the offspring they found those from the viable hybrids looked very similar to those of their parents, but the microbiomes of hybrids that did not survive looked “chaotic” and were completely different to those of their parents.

For the next stage of their study the researchers raised hybrid wasps in a microbe-free environment, to see how they would fare without a microbiome.

To their surprise, they found the germ-free hybrids fared just as well as non-hybrid larvae.

But when they transferred gut microbes from the regular hybrids to the germ-free ones, they found survival rates in the germ-free ones dropped significantly.

Jack Werren, an evolutionary geneticist at the University of Rochester in New York, describes Bordenstein and Brucker’s work as “important and potentially groundbreaking”.

He told Nature News the study shows that the problem of hybrid offspring is not just in their genes but in how their genes interact with the microbes they carry.

He says we now need to investigate which genes regulate which microbes and how this process is disrupted in hybrids.

An award from the National Science Foundation’s Dimensions of Biodiversity program helped fund the study.

A study published in 2012 also suggests that the DNA of gut microbes has a unique figerprint that can identify individuals as uniquely as their own cellular DNA.

Written by Catharine Paddock PhD