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Gut microbes keep species apart

Intestinal flora dooms hybrid offspring of cross-breeding wasps.

Closely-related organisms are often considered different species if they cannot produce viable offspring by interbreeding — and in the case of two wasp species, that barrier may lie at least in part in the gut flora. Credit: Micrograph by Robert M. Brucker

Mountain ranges and rivers can act as physical barriers that separate closely related species and keep them from cross-breeding. But the trillions of microbes in an animal’s guts could have the same role.

Robert Brucker and Seth Bordenstein, biologists at Vanderbilt University in Nashville, Tennessee, have found that the gut bacteria of two recently diverged wasp species act as a living barrier that stops their evolutionary paths from reuniting. The wasps have subtly different collections of gut microbes, and when they cross-breed, the hybrids develop a distorted microbiome that causes their untimely deaths.

“This is the most convincing evidence that the microbiome evolves with hosts over long time periods and might affect the speciation process,” says Bordenstein. The results are published in Science1.

Jürgen Gadau, an evolutionary biologist at Arizona State University in Tempe, says that the microbiome is just one of many factors that drive the origin of species. “The important point is that microbes can change very rapidly,” he says — so they could very quickly enforce the separation of nascent species.

It's what's on the inside that counts

“The gut microbiome has been intensely studied from a health perspective, but very little has been done on its evolution,” says Bordenstein. Other scientists have shown that the microbiomes of different species diverge in a way that mirrors their hosts' evolutionary relationships2, but it was unclear whether the bacteria were simply reacting to the hosts’ changing diets or were truly co-evolving with them.

Brucker and Bordenstein addressed this by studying Nasonia giraulti and Nasonia vitripennis, two parasitic wasps that deposit their eggs in the larvae of other insects. The two species diverged one million years ago, and can still raise their young on the same hosts. When they breed, around 90% of male offspring die as larvae. 

The researchers found that the wasps' gut microbes included a bacterium in the genus Providencia, and another species called Proteus mirabilis. The parental species had more Providencia, but P. mirabilis dominated in the hybrids. This suggests that interbreeding brings about harmful changes to the gut flora, so that the insects' microbiota helps to keep the two species separate.

To confirm that the different flora was responsible for the males' demise, the team tried ‘curing’ the hybrid wasps of their gut microbes. They devised a way of rearing Nasonia eggs in a nutrient broth rather than an insect host, and killed the microbes in the wasps' developing guts using antibiotics. This rescued many of the doomed hybrids: half survived to pupation. But when the team added Providencia and P. mirabilis to the rearing liquid of initially germ-free wasps, most of the hybrid larvae died as usual.

Genes and germs

“This is an important and potentially groundbreaking study,” says Jack Werren, an evolutionary geneticist at the University of Rochester in New York. “It reveals that problems in hybrids can be due not just to their genetic make-up, but to interactions between their genes and associated microbes.” The next step, he says, is to “determine which genes are involved in regulating which bacteria, and how this is disrupted in hybrids”.

Brucker and Bordenstein found that 40% of the wasps’ immune genes were at least twice as active in the normal hybrids as in the germ-free ones. They suspect that genetic incompatibilities between the parent species disrupt the hybrids’ immune systems and weaken their ability to control their gut microbes. The insects end up with an unusual microbiome, which kills them. “The closest analogy we have is that it’s like an autoimmune disorder,” says Brucker.

In this way, the insects' microbiota helps the two species to separate and, in time, to differentiate ever more, even if they share the same geographical range. Likewise, an earlier study3 showed that gut microbes can steer the sexual preferences of flies towards individuals with similar microbiomes, which might also help to accentuate the split between species.

“We’d never say that the microbiome is the key element in all speciation,” says Brucker. Rather, he feels that biologists must consider both the genome and the microbiome to understand animal evolution. “Our classic understanding of speciation is still true but we’re just adding a new arm to that,” he says.


  1. Brucker, R. M. & Bordenstein, S. R. Science (2013).

  2. Ochman, H. et al. PLoS Biol. 8, e1000546 (2010).

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  3. Sharon, G. et al. Proc. Natl Acad. Sci. USA 107, 20051–20056 (2010).

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Yong, E. Gut microbes keep species apart. Nature (2013).

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