The United States may be the home of multiculturalism, but American guts sport much less diversity than those of rural residents of Malawi and Venezuela. That's the conclusion of a new study, which finds that the protein-rich diet consumed by people in western countries may have a profound effect on the microbes they harbor. American gut populations also seem more adapted to a meat-rich diet.
In the body, microbes outnumber human cells by a factor of 10 to one. Research into these vast bacterial populations—together called microbiomes—is booming. Scientists have discovered that microbial boarders play a crucial role in breaking down certain nutrients in the diet and turning other molecules into a form that is useful to humans. The composition of the microbiome also impacts how susceptible a host is to certain diseases, they suspect.
To test that hypothesis, however, scientists first need to get a handle on what the microbiome of healthy adults looks like. So gastroenterologist Jeffrey Gordon at Washington University in St. Louis and his colleagues collected fecal samples from 532 individuals of all ages, more than half of them living across the United States, the rest Amerindians living in two villages in Venezuela and members of rural communities in Malawi. The researchers froze the samples, pulverized them, and extracted DNA. By picking out and sequencing 16S rDNA, a piece of DNA common to all microbes and used to classify them, the scientists could identify the species present in the gut microbial community.
They found that the microbiome in all three populations matured in a similar way: Infants started out with fewer microbe species, but at age three, the diversity of their microbiome had reached that of adults. "Like other organs, it takes the microbiome time to develop," says Dusko Ehrlich, a microbial geneticist at the National Institute for Agricultural Research in Paris who is coordinating a European project to establish associations between the genes of human intestinal microbes and disease.
The adult microbiomes of Amerindians and Malawians were surprisingly similar, the team reports online today in Nature, but those in the United States differed significantly. For one thing, they were much less diverse, harboring roughly 25% fewer species than Venezuelan microbiomes. Ehrlich calls that "a very strong and unexpected finding. … There seems to be a loss in diversity in Western microbiomes," he says.
By fully sequencing 110 of the samples, the researchers also found differences in which genes were represented in the microbiomes of adults in the three countries. Alpha-amylase, an enzyme involved in the breakdown of starch, was more common in the microbes found in samples from Malawi and Venezuela; U.S. microbiomes contained more genes involved in breaking down amino acids and simple sugars. The researchers speculate that the disparity reflects differences between the U.S. diet, rich in proteins and sugars, and those in Malawi and Venezuela, which are dominated by corn and cassava.
An analysis of the gut microbiome of 33 mammals done by Gordon's group and published in Science in 2011 also showed that microbiomes correlate with diet. Overall, Amerindian microbiomes most closely resemble those of herbivorous mammals, he says, while U.S. microbiomes look more like those found in carnivores. "At least one facet of our genetic landscape is being impacted by our Western diet," Gordon concludes. "What that means for the risk of disease will have to be ascertained in future studies."
Microbiologist Jonathan Eisen of the University of California, Davis, compares the work to the exploration of a new continent: "Everything is new, everything is discovery." But he thinks it's too early to single out diet as the causative factor behind the variation. "There are a million differences between these samples, now they have microbial differences to go with them, but we have no idea which change goes with which," he says.
David Relman, microbiologist at Stanford University School of Medicine in Palo Alto, California, also cautions against drawing broad conclusions. "Although the current study represents a heroic effort," he says, "we still have a long way to go before we have a truly global picture of variation in the human microbiome."