DNA Of Gut Microbes Has Unique Fingerprint

New research suggests the DNA of the vast collection of microbes in the gut has a unique figerprint that can identify individuals in the same way as human DNA.

The researchers, from Washington University School of Medicine in St. Louis, Missouri, in the US, and the European Molecular Biology Laboratory in Heidelberg, Germany, write about their study, believed to be the first to catalogue the genetic variation of microbes that live in the gut, in a paper published online in Nature on 5 December.

The Gut Microbiome

In recent years we have started to understand more about the microbes that colonize every nook and cranny of the human body. We now know that our "microbiome" comprises trillions of microorganisms that outnumber human cells by 10 to 1.

And we are beginning to learn how our microbial genes work together with our human genes to keep us healthy and, in some cases, cause disease.

The microorganisms that live in the human gut, the gut microbiome, extract nutrients from food, help synthesize vitamins, protect against infection and make compounds that reduce inflammation.

Individualized Collection

George Weinstock is associate director of The Genome Institute at Washington University, and corresponding author of the new Nature study. He describes in a press release how surprised they were to find that we can be identified by the collective DNA of our gut microbes.

"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 explains.

Genetic Variation of Microbial Genomes

For their study, Weinstock and colleagues analyzed microbial DNA from 252 stool samples taken from 207 people in the United States and Europe who were taking part in one of two projects that is cataloguing the human microbiome: the Human Microbiome Project, funded by the National Institutes of Health in the US, and the Human Intestinal Tract (MetaHIT) project, funded by the European Commission.

However, neither of these high profile projects has looked at the genetic variation of the microbial genomes in the body.

Weinstock and colleagues focused on 101 species of microbes commonly found in the gut and identified more than 10 million single-letter differences in their collective DNA.

And they found other DNA alterations, incuding insertions, deletions and differences in structure.

DNA of Gut Microbiome Remains Stable Over Time

The team also discovered that the DNA of the gut microbiome remains stable over time.

They could see this because 43 of the participants had given two stool samples at least a month apart (in most cases the second sample was collected six to twelve months after the first).

In those samples the researchers found little variability in the gut microbial DNA over time, even though the species of microbes themselves fluctuated.

"Even after a year, we could still distinguish individuals by the genetic signature of their microbial DNA," says Weinstock.

"The microbial DNA in the intestine is remarkably stable, like a fingerprint," he explains.

Microbiome Co-Evolves with Us

From the day we are delivered into the world as newborns we become colonized with microbes. Some we inherit from our mothers during birth, others from the environment.

Co-author Makedonka Mitreva, assistant professor of medicine at The Genome Institute at Washington University, says:

"The DNA of our microbes is a historical record of the microbial evolution in our bodies."

"Many of these organisms would have colonized us when we were very young and would have grown and evolved with us throughout our lifetimes," she adds.

But we are only just beginning to understand how this vast collection of organisms shapes our lives.

Researchers studying the gut microbiome suggest an imbalance of bacteria can lead to diseases like irritable bowel syndrome and Crohn's disease.

Gut bacteria may even play a role in obesity, as an animal study published in the Journal of Proteome Research in February 2012 suggests.

Scientists working on the NIH's huge Human Microbiome Project (HMP) have now mapped all the different microbes that live in and on a healthy human body. In June 2012 they published several papers including two in Nature and two in PLoS ONE revealing a number of remarkable discoveries, including evidence that harmful bacteria can live in healthy bodies and and co-exist with their host and other microbes without causing disease.

Mitreva says they hope further studies of the gut microbiome will help scientists find out how to manipulate their genes to improve human health and make drugs more effective.

Funds from the European Molecular Biology Laboratory, MetaHIT grants from the European Community's Seventh Framework Programme, and grants from the NIH helped finance the study.

Written by Catharine Paddock PhD
Source:MNT