30 July 2013

Our Destiny Lies Not in Our Stars, But in Our Bacteria

Think you know all about evolution (assuming you accept it)? We have a gut feeling there’s more to it than you think.


Color-enhanced scanning electron micrograph showing Salmonella typhimurium invading cultured human cells. (PHOTO: PUBLIC DOMAIN)

Strictly by the numbers, the vast majority — estimated by many scientists at 90 percent — of the cells in what you think of as your body are actually bacteria, not human cells. The number of bacterial species in the human gut is estimated to be about 40,000. ... The total number of individual bacterial cells in the gut is projected to be on the order of 100 trillion.
There’s been a lively academic debate—the “hologenomic theory of evolution”—drawn along these lines, wondering that if microbes are so much of us, surely they must affect our evolution. Hologenomic refers to a critter’s genetic package and that of its itty-bitty entourage, or as biologist Seth Bordenstein (“a scientist, educator, optimist, consultant, and non-linear thinker”) puts it, “the aggregate genome and microbiome of animals.” He and his colleagues at his Vanderbilt lab believe these combined sets of genetic stuff form a “persistent, evolutionary unit.”

Given the weight of biomatter in an animal, and the yeoman’s work these bugs do, it’s an intuitively sensible proposition. Still, until late it’s been somewhat of a microbiology wallflower, or perhaps Wallin-flower, since Ivan Wallin suggested something along the lines of such “symbiosis and speciation” in 1927.

To fast forward more than eight decades, here’s a recent tweet from Bordenstein: “Biologists no longer study if there r genomes in life’s structures but whether all those genomes r interconnected beyond self #hologenome

Bordenstein and his post-doc Robert Brucker concocted an elegant proof of this—their study appears online in the journal Science—using gut bacteria not from people but from three different species of a parasitic wasp.

Two of the species are believed to have diverged 400,000 years ago, the third about a million years ago. As a result, this gave the researchers two species with somewhat similar genomes and somewhat similar but not identical “microbiomes,” while the third species’ genome and microbiome were further removed. When the various species mate with each other, those differences are apparent—offspring from the two more closely related species tend to survive, while those from one of the close and the far species tend to die out over time. (Bordenstein has described these wide-gulf hybrids as having “chaotic and totally different” gut flora, hardly a recipe for thriving.)

Feeding the wasps sterile food so that the gut flora wouldn’t develop, Bordenstein and Brucker interbred the insects in the lab. The presence of the gut bacteria actually tamps down successful hybridization. Among what we might call the bug-less insects, the survival rate for hybrids was pretty much the same regardless of what pair of parents they had. If that’s interesting enough, as a sort of second stage check, when the gut bugs were introduced to the hybrids, the ones with the wider genetic (and microbiomic) gulf tended to not survive another generation.

“Our results move the controversy of hologenomic evolution from an idea to an observed phenomenon,” Bordenstein was quoted in a release from Vanderbilt. “The question is no longer whether the hologenome exists, but how common it is?” And while the research has been met with interest, not everyone accepts the whole of the hologenomic concept yet. As evolutionary geneticist John Werren—who considers this wasp work important—asked Science’s Kai Kupferschmidt, “They are not co-evolving as a single unit, so why would we call them a single genome?”

But for those of us not on the frontlines of microbiology, whether hologenomic or not, the title of Valerie Brown’s piece seems more accurate than ever: “Bacteria R Us.”

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