Gut Microbiome: 11 Genetic Regions Linked to Bacteria & Disease Risk

Our genes play a surprisingly significant role in shaping the complex community of microorganisms living in our gut, according to two new international studies involving nearly 28,000 individuals. Researchers have identified 11 genetic regions that demonstrably influence both the types of bacteria present in the gut – the gut microbiome – and the functions those bacteria perform. This represents a substantial leap forward in understanding, as previously only two such genetic regions were known.

The gut microbiome, the trillions of bacteria, fungi, viruses, and other microbes residing in our digestive tract, has emerged as a critical area of health research. Its composition is increasingly linked to a wide range of conditions, from digestive health to immune function and even mental wellbeing. However, disentangling the relative contributions of genetics and environmental factors – diet, lifestyle, medication – in determining microbiome composition has been a major challenge. These new studies begin to clarify that genetic influence.

Uncovering Genetic Links to Gut Bacteria

The research, conducted by international teams and published in Nature Genetics, involved analyzing genetic data and gut bacteria samples from a large and diverse cohort of over 28,000 people. Researchers meticulously surveyed the bacterial species present in each participant’s gut, then correlated this information with their genetic profiles. The analysis pinpointed 11 distinct genetic regions that exhibited a clear association with specific bacterial compositions and functions.

“We have learnt a lot about the role played by genetics in the gut microbiome,” explains Tove Fall, Professor of Molecular Epidemiology at Uppsala University, who led one of the studies. “Several of the genetic connections that we found have to do with very specific biological mechanisms. These concern, for instance, which molecules are present on the surface of gut cells and are thereby available as food for bacteria. They also relate to the way in which the gut reacts to molecules produced by bacteria.”

Connections to Disease Risk

Importantly, the researchers also observed connections between some of the identified genetic variants and an increased risk of specific health conditions. These included gluten intolerance, haemorrhoids, and cardiovascular diseases – conditions already suspected to have links with the gut microbiome. This suggests that variations in gut bacteria composition, driven by genetic predisposition, may contribute to the development of these diseases.

“We saw that some of these genetic variants were linked to the risk of gluten intolerance, haemorrhoids and cardiovascular diseases,” says Claes Ohlsson, Professor at the University of Gothenburg, who co-led the other study with Kristian Hveem, Professor at the Norwegian University of Science and Technology (NTNU). “This suggests that changes in the composition of intestinal bacteria could provide a way to better understand how genetic risks affect health.”

Beyond the Gut: Genetic Influence on Oral Microbiome

Interestingly, research published in late January 2026 also revealed a genetic link to the microbiome found in the mouth. Scientists at the Broad Institute and Mass General Brigham discovered that 11 regions of the human genome influence the abundance of dozens of bacterial species in the oral cavity. This study, analyzing the largest collection of oral microbiome profiles to date, even identified a connection between a specific human gene, AMY1, and oral health, including potential impacts on cavity risk and denture use.

This finding highlights the broader implications of genetic influence on microbial communities throughout the body, not just within the gut. The researchers found genome-to-genome interactions between human DNA and the DNA of the oral microbiome, suggesting a complex interplay between our genes and the microbes we host.

Building a Resource for Future Research

The studies relied on access to large “biobanks” – collections of biological samples and associated data. The gut microbiome biobanks used in this research are among the largest in the world, providing a valuable resource for future investigations. Researchers emphasize the potential for these resources to drive the development of new strategies for preventing and treating disease by targeting the gut microbiome.

Given that many aspects of our health are linked to the gut microbiome, we naturally want our research to contribute to better ways of preventing and treating diseases by paying attention to the interaction between genes, gut biology and the microbiome.

Tove Fall, Professor of Molecular Epidemiology, Uppsala University

While these findings represent a significant step forward, it’s important to note that the relationship between genes, the gut microbiome, and disease is complex and multifaceted. Further research is needed to fully elucidate the mechanisms involved and to determine how this knowledge can be translated into practical clinical applications. The identification of these genetic regions, however, provides a crucial foundation for future studies aimed at understanding and manipulating the gut microbiome to improve human health.