Genetics Does Influence the Gut Microbiome, Long Term Research Reveals

Gut microbiome, the collective population of bacteria, viruses, fungi, and other microbes in our gastrointestinal tract, has been implicated in regulating our hormones, behavior, response to drugs, and susceptibility to certain diseases.

Over several research paradigms, we understand the role of the gut microbiome in health and disease, but we do not fully realize the determinants and their effects on the microbiome. Some studies suggest that the environment largely shapes the microbiome.

The Gut Microbiome is Heritable

In a new study published in Science, scientists from Notre Dame University, Duke University, and the University of Minnesota demonstrate the genetic heritability of the gut microbiome. Profiling the microbiome from over 500 wild baboons from fecal samples collected over 14 years, the authors could understand the link between diet, environment, and genetics in shaping and altering the gut biome.

They found that genetically related samples had 95% similarity in diversity and abundance of specific populations in their gut microbiome, indicating that it is heritable, albeit low (0.068). Heritability is a measure of the role of genetics for a given trait. A heritability of 1 means that genetic factors can explain all variation, while heritability of 0 indicates that the trait is not governed by genetics.

Stark Contrast to Previous Study Results

This is a marked change from previous human studies, which demonstrated that genetics do not determine the gut microbiome. However, this discrepancy could be explained because of the limited sample size and ‘snapshots’ of microbiome studied in humans- all studies analyzed samples collected at a single time point.

This study in baboons collected samples over a long period, with additional data on their social behavior, diet, and other factors, which enabled the linkage. Since baboons and early humans shared the same environment, their gut microbiomes are expected to be similar and under similar evolutionary pressures. This study was made possible due to the Amboseli Baboon Project at Kenya’s Amboseli National Park, which has collected samples and data on their baboon population since 1971.

Dynamic Microbiome Heritability

Strikingly, the authors also found a correlation between host traits such as age, sex, and environment in changing the gut microbiome, indicating that microbiome heritability is dynamic. Heritability was higher in the dry season and in older animals.

The study gives us a comprehensive and quantitative list of determinants that govern microbiome composition and places genetics as the baseline, indicating that gut microbiomes may evolve based on natural selection pressures on the host.

This helps delineate the linkage and genetic basis of microbes involved in disease outcomes. The authors insist that their results are consistent with the prevailing notion that environment and behaviors are major determinants of the microbiome and add that genetics may help explain the factors that drive long-term maintenance of the microbiome.

Lead author, Professor Elizabeth Archie at Notre Dame, said, “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.”

Future studies in humans should account for long-term and large sample sizes to dissect microbiome heritability and selection.

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Author

Sahana Shankar