Gut microbes identified as new genetic fingerprint

A new study has suggested that just as human DNA varies from person to person, so too does the massive collection of microbial DNA in the intestine

The research was conducted by researchers at Washington University School of Medicine in St. Louis and the European Molecular Biology Laboratory in Heidelberg, Germany

It is the first to catalog the genetic variation of microbes that live in the gut, where they extract nutrients from food, synthesize vitamins, protect against infections, and produce compounds that naturally reduce inflammation.

The widespread genetic diversity uncovered by the scientists can help them understand how our microbial genes work together with our human genes to keep us healthy or, in some cases, to cause disease

“Surprisingly, each of us can be identified by the collective DNA of our gut microbes,” said corresponding author George Weinstock, PhD, associate director of The Genome Institute at Washington University

“That collection is individualized, completely analogous to our human genome. Differences in the way individuals respond to various drugs or the way they use specific nutrients can be traced to the genetic variation in our microbial genes as well as in our human genes,” he stated

The researchers analyzed the microbial DNA in 252 stool samples from 207 individuals living in the United States and Europe.

All the subjects had participated in one of two recent high-profile initiatives to catalog the diverse species of microbes that live in and on the body. Neither of those studies – the Human Microbiome Project, funded by the National Institutes of Health, and the Metagenomics of the Human Intestinal Tract (MetaHIT) project, funded by the European Commission – looked at the genetic variation of the microbial genomes in the body

For the new study, the researchers zeroed in on 101 species of microbes commonly found in the intestine, identifying more than 10 million single-letter changes in the collective DNA of those microbes. They also found numerous other DNA alterations, including insertions, deletions and structural changes

In 43 subjects for whom the researchers had two stool samples collected at least a month apart (most were collected six months to a year after the initial sample), the researchers found very little variability in the microbial DNA over time, although the species of microbes in the intestine fluctuated

“The microbial DNA in the intestine is remarkably stable, like a fingerprint. Even after a year, we could still distinguish individuals by the genetic signature of their microbial DNA,” said Weinstock

With this new catalog, the researchers can begin to understand the selective forces that shape the microbiome – the collection of microbes and their genes – in the intestine

The study was recently published online in Nature.