What is already known
The gut microbiota is essential for health as it influences metabolism, immunity and even behavior. However, traditional methods of studying the community of microbes living in the gut have struggled to connect specific bacteria to conditions such as obesity and diabetes.
What this research adds
Researchers analyzed about 4,000 metagenomic samples from 38 studies spanning 15 diseases over a decade and across three continents. They identified a core microbiota signature marked by two competing bacterial groups, called C1A and C1B, which are linked to a person’s health. C1A is enriched with genes for the digestion of fiber and the production of beneficial metabolites, while C1B contains antibiotic resistance and virulence genes. Dietary fiber influences the balance between these bacterial groups, the researchers also found.
Conclusions
The study identified a core microbiota signature that may serve as a health indicator and a therapeutic target.
The gut microbiota is essential for health as it influences metabolism, immunity and even behavior. An analysis of about 4,000 metagenomic samples has now revealed a core set of gut microbes that may be important for human health.
The findings, published in Cell, suggest that this core microbiota signature can serve as a health indicator and a therapeutic target.
“Our research identifies the bacteria in the gut that stay connected, no matter what challenges the body faces, such as dietary changes or illness,” says study senior author Liping Zhao at Rutgers University in New Brunswick, New Jersey. “By focusing on these resilient and interconnected bacteria, we’ve developed a new method for pinpointing the microbes that are most crucial for maintaining our health.”
Thanks to improvements in DNA sequencing, scientists can now explore what types of bacteria live in the gut and what they do. However, traditional methods of studying the gut microbiota have struggled to connect specific microbes to conditions such as obesity and diabetes.
To identify a core gut microbiota that is linked to a person’s health, Zhao and his team analyzed metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 studies spanning 15 diseases over a decade and across three continents.
Competing guilds
Data from the high-fiber dietary intervention trial revealed stable interactions among 477 gut microbes organized in two competing groups, C1A and C1B. The bacterial group C1A, also called the “foundation guild”, is enriched with genes for fiber digestion and short-chain fatty acid production, while C1B , also called the “pathobiont guild”, contains antibiotic resistance and virulence genes.
The foundation guild is essential for stabilizing the gut microbiota and supporting the gut barrier, reducing inflammation, the researchers found. Short-chain fatty acid are known for their beneficial effects on a person’s health.
Although microbes from the pathobiont guild can help the immune system to recognize harmful bacteria when present in low quantitites, they can drive disease when their levels increase above a certain threshold, the researchers say.
Targeted therapies
Further analyses showed that dietary fiber influences the balance between the two bacterial guilds, with C1A increasing and C1B decreasing during the intervention. This shift in abundance of the two microbial guilds was linked to improved metabolic outcomes in people with diabetes, the researchers found.
Next, the team developed a tool that uses the core gut microbiota signature to help diagnose different diseases, showing it can be a general indicator of health. This tool also helped predict how well treatments would work for conditions such as inflammatory bowel diseases, rheumatoid arthritis and melanoma.
“Understanding these core microbial interactions provides valuable insights into the essential functions of the gut microbiome and its role in health and disease,” the authors say. “It also offers a robust framework for developing targeted microbiome- based therapies.”
