Commensal bacteria are found throughout an organism, but it is not known whether associations between gut bacteria and their host are heritable. In a new study, biologists from the University of Notre Dame and elsewhere examined changes in the microbiomes of 585 wild baboons from samples collected over 14 years in Kenya’s Amboseli National Park; almost all microbiome traits tested demonstrated some level of statistically significant heritability; the researchers also found that several of the microbiome traits heritable in baboons are also heritable in humans.
Grieneisen et al. analyzed 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Image credit: Darryl Leja, National Human Genome Research Institute, National Institutes of Health.
“The environment plays a bigger role in shaping the microbiome than your genes,” said Professor Elizabeth Archie, a researcher in the Department of Biological Sciences at the University of Notre Dame.
“But what our study does is move us away from the idea that genes play very little role in the microbiome to the idea that genes play a pervasive, if small, role.”
The gut microbiome performs several jobs. In addition to helping with food digestion, it creates essential vitamins and assists with training the immune system.
Previous studies on the gut microbiome in humans showed only 5-13% of microbes were heritable, but Professor Archie and colleagues 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 looked at 16,234 gut microbiome profiles from 585 wild Amboseli baboons.
The microbiome profiles from the samples showed variations in the baboons’ diets between wet and dry seasons.
The scientists found that 97% 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% — 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.
“This really suggests that in human work, part of the reason researchers haven’t found that heritability is because in humans they don’t have a decade and half of fecal samples in the freezer, and they don’t have all the initial host (individual) information they need to tease these details out,” Professor Archie said.
Microbiome heritability was typically 48% 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.
“Because the study also showed the significant impact of environment on the gut microbiomes in baboons, our findings agreed with previous studies showing that environmental effects on the variation in the gut microbiome play a larger role than additive genetic effects,” the authors said.
Their findings appear this week in the journal Science.
Laura Grieneisen et al. 2021. Gut microbiome heritability is nearly universal but environmentally contingent. Science 373 (6551): 181-186; doi: 10.1126/science.aba5483