The human gut is home to trillions of microorganisms (the microbiome), a vast community that helps shape digestion, immune function and metabolism. Now, researchers led by the University of Vienna have found that many gut bacterial species are more complex than they appear.
Using an analytical strategy known as ‘reverse ecology,’ the team showed that individual bacterial species can contain several evolutionarily distinct populations, each adapted to different conditions inside the gut. Some of these populations were associated with advanced age, chronic inflammatory bowel diseases, colorectal cancer and type 2 diabetes.
The findings, published in Nature, could help scientists identify more precise microbiome biomarkers and may eventually support treatments aimed at specific bacterial populations rather than entire species.
Looking Beyond Bacterial Species
Most microbiome research groups bacteria by species or by broad genetic similarity. These categories are useful, but they can overlook important differences between populations that have adapted to different environments within the human body.
That can make it difficult to determine which bacteria are genuinely associated with disease, which are simply present by coincidence, and which may have protective effects.
The researchers therefore asked whether they could identify more biologically meaningful bacterial groups by looking for evidence of adaptation and specialization within the gut.
Tracking Evolution Through Genetic Data
The team examined thousands of bacterial isolates collected from the human gut, along with large amounts of metagenomic data from people in multiple countries and across different age and health groups. Metagenomic data includes the complete genetic information of microbial communities in the sample.
To analyze these data, the researchers developed a bioinformatic method based on ‘reverse ecology,’ an approach that uses genomic information to infer how organisms have adapted to particular environments.
The goal was to identify genetic signatures showing that certain bacterial populations had successfully adapted to specific ecological niches inside the gut.
Hidden Lineages Within Familiar Gut Bacteria
One especially important clue came from signs of so-called ‘genome-wide selective sweeps.’ These occur when an individual gains a beneficial mutation that gives it an advantage over closely related individuals, allowing its descendants to become dominant.
This process reduces genetic diversity within the successful population. At the same time, it can create groups that are highly similar in both ancestry and biological function, making them easier to distinguish from neighboring populations.
The analysis revealed that many well-known gut bacterial species actually divide into several distinct evolutionary lineages. These populations appear to be better suited to different conditions within the gut.
“If you don’t just count species but take evolutionary adaptation into account, you can identify the biologically relevant units in the microbiome much more accurately,” says lead author Xiaoqian Annie Yu, Centre for Microbiology and Environmental Systems Science (CeMESS), University of Vienna. “Even within the same bacterial species, some populations occur more frequently than others in certain diseases. When all are considered together, this often remains hidden.”
Gut Bacteria Can Spread Across Continents
The researchers also uncovered evidence that particularly competitive bacterial populations can spread rapidly across large geographic distances. In some cases, these populations appear to have expanded across continents within only a few decades.
Patterns like this have previously been observed mainly among pathogens, making the finding especially notable for ordinary gut bacteria.
“Our findings show that gut bacteria are also more dynamic than previously thought. Well-adapted strains can spread internationally and occupy new ecological niches,” says study leader Martin F. Polz from the University of Vienna.
The results suggest that the gut microbiome may be shaped by more than diet, medication and lifestyle. Transmission between people could also be an important force influencing which bacterial populations become established and spread.
Toward More Precise Microbiome Medicine
The discovery could change how researchers connect gut bacteria with disease. Instead of treating an entire bacterial species as a single unit, scientists may eventually be able to focus on the specific populations that are most relevant to health.
That added precision could improve the search for biomarkers and, over time, may lead to more targeted therapies. Such treatments could potentially encourage beneficial bacterial strains while suppressing populations associated with harmful effects.
The researchers now plan to determine which genes separate these bacterial populations from one another and what biological functions those genetic differences produce.
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