Our genes shape our gut bacteria, new research shows
Taken together, the bacteria, viruses, fungi and other microbes that live in our intestines form the gut microbiome, which plays a key role in the health of people and animals. In new research from Duke University, the University of Minnesota, and the University of Notre Dame scientists found that genetics nearly always plays a role in the composition of the gut microbiome of wild baboons.
In the study published recently in Science under the leadership of Jenny Tung and collaborators at Duke, UNM and Notre Dame, reserachers discovered that most bacteria in the gut microbiome are heritable after looking at more than 16,000 gut microbiome profiles collected over 14 years from a long-studied population of baboons in Kenya’s Amboseli National Park. However, this heritability changes over time, across seasons and with age. The team also found that several of the microbiome traits heritable in baboons are also heritable in humans.
The gut microbiome performs several jobs. In addition to helping with food digestion, it creates essential vitamins and assists with training the immune system. This new research is the first to show a definitive connection with heritability.
Previous studies on the gut microbiome in humans showed only 5 to 13 percent of microbes were heritable, but Archie and the research team hypothesized the low number resulted from a “snapshot” approach to studying the gut microbiome: All prior studies only measured microbiomes at one point in time.
In their study, the researchers used fecal samples from 585 wild Amboseli baboons, typically with more than 20 samples per animal. Microbiome profiles from the samples showed variations in the baboons’ diets between wet and dry seasons. Collected samples included detailed information about the host, including known descendants, data on environmental conditions, social behavior, demography and group-level diet at the time of collection.
The research team found that 97 percent of microbiome traits, including overall diversity and the abundance of individual microbes, were significantly heritable. However, the percentage of heritability appears much lower — down to only 5 percent — when samples are tested from only a single point in time, as is done in humans. This emphasizes the significance of studying samples from the same host over time.
The team did find evidence that environmental factors influence trait heritability in the gut microbiome. Microbiome heritability was typically 48 percent higher in the dry season than in the wet, which may be explained by the baboons’ more diverse diet during the rainy season. Heritability also increased with age, according to the study.
Because the research also showed the significant impact of environment on the gut microbiomes in baboons, their findings agreed with previous studies showing that environmental effects on the variation in the gut microbiome play a larger role than additive genetic effects. Combined with their discovery of the genetic component, the team plans to refine its understanding of the environmental factors involved.
But knowing that genes in the gut microbiome are heritable opens the door to identifying microbes in the future that are shaped by genetics. In the future, therapies could be tailored for people based on the genetic makeup of their gut microbiome.
In addition to Tung, other authors include fellow principal investigators Ran Blekhman of the University of Minnesota and Elizabeth Archie of Notre Dame; Mauna Dasari, Johannes Björk and David Jansen of the University of Notre Dame; former Notre Dame graduate student Laura Grieneisen; Trevor Gould of the University of Minnesota; Jean-Christophe Grenier, Vania Yotova and Luis B. Barreiro of Centre Hospitalier Universitaire Sainte-Justine Research Center; Neil Gottel and Jack Gilbert of the University of California, San Diego; Jacob B. Gordon, Laurence R. Gesquiere and Susan C. Alberts of Duke University; Niki H. Learn of Princeton University; and Tim L. Wango, Raphael S. Mututua, Kinyua Warutere and Long’ida Siodi of the Amboseli Research Project.
This research was supported by funding from the National Institutes of Health, Duke’s Population Research Center and Center for Population Health and Aging, the University of Minnesota Grand Challenges Biology Postdoctoral Fellowship, and the University of Notre Dame’s Eck Institute for Global Health.