The human gut is home to a vast community of trillions of microorganisms (the microbiome), which helps shape digestion, immune function, and metabolism. In addition to diet and medications, infection from person to person can also play a significant role in shaping the microbiome.
A team of researchers from the University of Vienna used a method called “reverse ecology” to show that many known species of gut bacteria actually consist of several evolutionarily distinct groups, each adapted to different conditions within the gut. Some of these bacterial populations are associated with aging, chronic inflammatory bowel disease, colorectal cancer, and type 2 diabetes. The findings, published in the journal Nature, may ultimately help improve the search for biomarkers and, in the long term, facilitate more precise treatments.
Most microbiome studies group bacteria by entire species or by shared genetic similarities. These categories are useful, but they can overlook distinct populations that have evolved to thrive in specific conditions within the human body. This makes it difficult to determine which bacteria are associated with disease, which are simply present by chance, and which may contribute to health protection. A central question is whether scientists can identify more precise biological entities that have evolved through adaptation and occupy distinct ecological niches in the gut.
The research team analyzed thousands of bacterial isolates from the human gut, as well as extensive metagenomic data—complete genetic information about the microbial communities in a sample collected from people from different countries, age groups, and health statuses.
Using a recently developed bioinformatics method within the framework of “reverse ecology”—an approach that infers ecological adaptations from genomic data—the researchers searched for genetic signatures of successful adaptation.
Signs of so-called genome-wide selective biases provided important clues. These events occur when one individual acquires a beneficial mutation and then outcompetes closely related individuals.
This process reduces diversity, but also leads to the formation of populations whose members are very similar in both origin and function, allowing them to be clearly distinguished in the dataset. The analysis revealed that many known species of gut bacteria have diverged into several such lineages. These populations appear to differ in the conditions in which they thrive.
“By considering not only species counts but also evolutionary adaptations, we can identify biologically significant units in the microbiome much more accurately,” says lead study author Xiaoqian Annie Yu of the Center for Microbiology and Environmental Sciences (CeMESS) at the University of Vienna. “Even within the same bacterial species, some populations are more common than others in certain diseases. When all these factors are considered together, this often goes unnoticed.”
The researchers also found evidence that highly competitive bacterial populations can quickly spread across continents, in some cases in just a few decades. Until now, this pattern has been observed primarily in pathogenic microorganisms.
“Our results show that gut bacteria are also more dynamic than previously thought. Well-adapted strains can spread globally and occupy new ecological niches,” says study leader Martin F. Polz of the University of Vienna.
These findings suggest that the microbiome is shaped not only by diet, medications, or lifestyle, but also by the transmission of infection from person to person.
This study opens new avenues for studying the microbiome. Instead of linking entire bacterial species to diseases, scientists will ultimately be able to focus on specific populations that are most important. This could improve the search for biomarkers and, in the long term, help make therapy more precise, for example, by promoting the growth of beneficial bacterial strains or reducing the abundance of problematic ones.
The team next plans to study which genes distinguish the identified populations from each other and what biological functions these genes may control.
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