Compared with Apes, People’s Gut Bacteria Lack Diversity, Study Finds

The microbes living in people’s guts are much less diverse than those in humans' closest relatives, the African apes, an apparently long evolutionary trend that appears to be speeding up in more modern societies, with possible implications for human health, according to a new study.

Based on an analysis of how humans and three lineages of ape diverged from common ancestors, researchers determined that within the lineage that gave rise to modern humans, microbial diversity changed slowly and steadily for millions of years, but that rate of change has accelerated lately in humans from the U.S.

People in non-industrialized societies have gut microbiomes that are 60 percent different from those of chimpanzees. Meanwhile, those living in the U.S. have gut microbiomes that are 70 percent different from those of chimps.

"It took millions of years, since humans and chimpanzees split from a common ancestor, to become 60 percent different in these colonies living in our digestive systems," said Howard Ochman, professor of integrative biology in the College of Natural Sciences at The University of Texas at Austin and co-author of the study. "On the other hand, in apparently only hundreds of years — and possibly a lot fewer — people in the United States lost a great deal of diversity in the bacteria living in their gut."

That rapid change might translate into negative health effects for Americans. Previous research has shown that compared with several populations, people living in the U.S. have the lowest diversity of gut microbes. Still other research has linked a lack of microbial diversity in human guts to various diseases such as asthma, colon cancer and autoimmune diseases.

The results of this latest study, carried out by researchers from The University of Texas at Austin, Yale University, the University of Pennsylvania and elsewhere, appear this week in the journal Proceedings of the National Academy of Sciences. The lead author is Andrew Moeller, a visiting scholar at The University of Texas at Austin and a graduate student at Yale University.

One possible explanation for humans evolving to have less diversity in their gut microbiomes is that they shifted to a diet with more meat and fewer plants. Plants require complex communities of microbes to break them down, which is not as true for meat.

As for why Americans have experienced much more rapid changes in microbial diversity compared with people in less industrialized societies, some experts have suggested more time spent indoors, increased use of antibacterial soaps and cleaners, widespread use of antibiotics and high numbers of births by Cesarean section all may play a role. Antibiotics and antimicrobial cleaners can kill good bacteria along with the bad, and C-section deliveries prevent babies from receiving certain bacteria from the mother typically conferred during vaginal births.

"Declining diversity in the gut has been a trend for a long time," said Ochman. "It's tantalizing to think that the decrease in microbial diversity in humans is due only to modern medical practices and other lifestyle changes, but this research shows other factors over time also must have played a role."

The researchers analyzed the genetic makeup of bacteria in fecal samples from humans, chimpanzees, bonobos and gorillas to draw their conclusions.

Moeller and Ochman's co-authors are Yingying Li at the University of Pennsylvania; Eitel Mpoudi-Ngole at the Institut de Recherches Médicales et d’Études des Plantes Médicinales, Prévention du Sida au Cameroun (Republic of Cameroon); Steve Ahuka-Mundeke at Institut National de Recherche Biomédicale (Democratic Republic of Congo) and the University of Montpellier (France); Elizabeth Lonsdorf at Franklin & Marshall College; Anne Pusey at Duke University; Martine Peeters at the University of Montpellier; and Beatrice Hahn at the University of Pennsylvania.

This work was supported by grants from the National Institutes of Health, the National Science Foundation, Agence Nationale de Recherche sur le Sida and the Jane Goodall Institute.

Download the paper "Rapid changes in the gut microbiome during human evolution" (PNAS, November 3,2014) at: http://www.pnas.org/content/early/2014/10/29/1419136111.full.pdf+html

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Humans, chimpanzees, bonobos and gorillas share common ancestors that lived millions of years ago. Scientists have long speculated that as humans evolved along a different path from the other apes, they lost much of their ancestral microbial diversity. This is the first statistically significant study to confirm that hypothesis.

"In this study we were able to compare hundreds of humans to hundreds of wild apes," said Andrew Moeller, visiting scholar at The University of Texas at Austin, graduate student at Yale University and lead author of the study. "That gave us the statistical power to actually test whether there is a difference between the species. We couldn't have done that before because we just didn't have enough samples."

The data on humans came from three earlier studies that compared human populations living in Venezuela, Malawi and the U.S. with a wide range of lifestyles including urban, rural and pre-industrial. Using the same data but with a different method of analysis, this latest study confirms earlier research which showed that people living in the U.S. have a much lower microbial diversity than any other population studied.

"There's something interesting going on with humans from the U.S.," said Moeller.

The study also showed that human gut microbiomes, the communities of microbes living in our guts, seem to be specialized for a meat-based diet. Compared with apes, humans have a very high abundance of a particular group of bacteria called Bacteroides, which are known to be associated with meat eating.

"It was surprising that, compared to apes, every human population showed the same general pattern of lower microbial diversity and higher levels of Bacteroides," said Moeller. "These are humans separated by thousands of miles and living vastly different lifestyles."

The three studies that provided the human data used in this latest study are:

Human gut microbiome viewed across age and geography (Nature, May 9, 2012)

A human gut microbial gene catalog established by metagenomic sequencing (Nature, March 4, 2010)

Gut microbiome of the Hadza hunter-gatherers (Nature Communications, April 15, 2014)