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UK Researchers Find Genomes of Two Bacterial Species Merging

NEW YORK (GenomeWeb News) – In an apparent reversal of the speciation process, two distinct bacterial species are becoming one — and intensive agriculture is likely a driving force in the convergence, researchers said.
 
In a paper published online today in Science, researchers from the University of Oxford used a technique called multi-locus sequence typing to compare two pathogenic species of bacteria, Campylobacter jejuni and Campylobacter coli. The team found gene flow patterns pointing to an unexpected “despeciation” that they attributed to the microbes' exposure to a new, shared, human-generated ecological niche.
 
“This is the first time anyone has shown anything like this,” senior author Martin Maiden, who studies bacterial population structure and public health at the University of Oxford, told GenomeWeb Daily News today.
 
The findings came out of a project originally aimed at characterizing C. jejuni and C. coli genes in order to understand the epidemiology of human Campylobacter infections. Together, the two bugs cause most of the bacterial cases of gastroenteritis, an inflammation of the gastrointestinal tract characterized by abdominal pain, fever, chills, and diarrhea that may become bloody.
 
But the team got some unexpected results when they analyzed multi-locus sequence typing data on seven C. jejuni and C. coli loci: they found a population of hybrid bacteria whose genomes had merged, seemingly reversing the process of speciation. Interestingly, gene flow doesn’t seem to happen equally between the two species. In most cases, C. coli apparently imports C. jejuni alleles.
 
While most of the Campylobacter detected are not hybrids, Maiden explained, the hybrid population is stable enough to detect. And, though genetic exchange between different bacterial species is common, this situation is particularly intriguing because large parts of chromosomes are being traded in a manner that indicates that the two distinct species, which have a shared ancestor, are re-merging.
 
“Interestingly, the other bacteria we’ve studied to a great extent are not doing this,” Maiden said. Still, he added, the phenomenon may occur, undetected, in other bacterial species. “It’s probably not normal, but that doesn’t mean this is the only example,” he said, noting that detecting other examples, if they exist, will require extensive sampling.
 
The results are particularly telling, the researchers said, because the processes of bacterial evolution and speciation are murky. In a sense, this paper provides clues about speciation in reverse: the evolutionary forces and events that once led to the speciation of C. jejuni and C. coli are no longer acting as strongly in some environments.
 
“What it sort of says is that it’s the existence of the unique ecosystems that maintain the species, not the other way around,” lead author Samuel Sheppard, an evolutionary microbiologist at the University of Oxford, told GenomeWeb Daily News today.
 
For instance, the team found that genetic changes leading to convergence are at least four times more common than those leading to divergence. “The forces causing them to diverge … are much less than the forces that cause them to converge,” Sheppard said.
 
And while it’s also unclear how rapidly the despeciation is happening, the researchers suggest that the hybrids are arising as a result of new, human-created ecosystems as opposed to genetic exchange in wild animal or bird populations.
 
In particular, the researchers speculate that agriculture — especially the domestication of livestock animals — has created situations in which the bugs share environments and swap genes, fueling despeciation. Still, they noted, more sampling from different environments will be necessary to confirm this.
 
Even so, the researchers said, the work highlights the unexpected consequences for other organisms — even microbes — that can occur when environments change. “Pre-existing environments have been degraded, and novel ones, such as intensive farms or acid mine drainage areas, have been created that provide a new adaptive landscape and opportunities for hybrid forms to evolve,” the authors wrote.
 
“As human beings, we have to be mindful that we are having a huge impact on the landscape,” Sheppard said.
 

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