And everybody has one favorite

By Tina Hesman Saey

Web edition: April 20, 2011
Print edition: May 21, 2011; Vol.179 #11 (p. 14)

There are three types of people in this world, and by their bacteria ye shall know them.

A consortium of researchers from Europe and Japan examined the DNA profiles of bacteria in fecal samples taken from 39 people belonging to six different nationalities. Each had a diverse group of microbes, but closer analysis revealed that the bacteria fall into three major types of communities, the researchers report online April 20 in Nature.

Previous studies had suggested that each person may have their own unique mix of intestinal microbes, but the new study takes “a more sophisticated” look, says George Weinstock, a geneticist at Washington University in St. Louis. Identifying distinct conglomerates of bacteria will aid scientists in determining if certain mixes of microbes contribute to health and disease, says Weinstock, who was not involved with the study. “That’s going to be terribly important for understanding why people are different and why they react differently to the environment or things like drugs and diet.”

Each of the newly identified microbial mixes — called enterotypes — is named for the dominant type of bacteria in the group. People with the Bacteroides enterotype have an abundance of Bacteroides bacteria and several associated types of bacteria, while people with the Prevotella and Ruminococcus enterotypes have more of those bacteria. The Ruminococcus type was the most common of the three.

People from Japan, Europe and the United States all fell into one of the three categories. The researchers didn’t find any correlation between a person’s enterotype and the person’s age, body weight, nationality, geographic location or diet. “We still don’t know what is driving these three types,” says Peer Bork, a bioinformatician at the European Molecular Biology Laboratory in Heidelberg, Germany. He and his colleagues speculate that the different communities may form around key bacteria that dispose of excess hydrogen in the form of methane or hydrogen sulfide. Another possibility is that the first organisms to colonize a person’s intestines may determine the community makeup. Or a person’s immune system may determine which microbes are allowed to settle in.

Although the species mix wasn’t linked to any particular human trait, certain groups of genes or biochemical functions carried out by the bacteria did match up with traits. “I can roughly tell you how old you are if you give me a stool sample,” Bork says. Body mass index also correlated with the presence of certain microbial genes and biological processes.

How bacteria use their genes is probably more important than which species are present, says Jeremy Nicholson of Imperial College London. “There’s this obsession with microbial speciation, which bugs do what,” he says, “but what is actually important is the capabilities of the microbial community as a whole.”

The researchers don’t yet know if a person’s enterotype changes over time or stays the same throughout life, or if certain enterotypes predispose people for diseases.