Your Gut Microbiome May Spread Between People, University of Vienna Study Finds

The human gut hosts trillions of microorganisms, together known as the microbiome, that help shape digestion, immune function and metabolism. A team led by the University of Vienna used a method called 'reverse ecology' — which infers ecological adaptations from genomic data — to show that many familiar gut bacterial species actually consist of several evolutionarily separate lineages, each adapted to different conditions inside the gut. The findings are published in Nature.

The researchers analyzed thousands of bacterial isolates from the human gut, along with metagenomic data — the complete genetic information of microbial communities — from people across different countries, ages and health groups. They looked for genetic signs of 'genome-wide selective sweeps,' events in which one individual gains a useful mutation and outcompetes closely related individuals, reducing diversity but producing populations highly similar in both ancestry and function. Many known gut bacterial species split into several such lineages, which differ in the conditions where they thrive best.

Some of these bacterial populations are linked with older age, chronic inflammatory bowel diseases, colorectal cancer and type 2 diabetes, said lead author Xiaoqian Annie Yu of the University of Vienna's Center for Microbiology and Environmental Systems Science. '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,' Yu said, adding that some populations occur more frequently than others in certain diseases, a pattern that can remain hidden when whole species are counted together.

The researchers also found that highly competitive bacterial populations can spread quickly across continents, in some cases within only a few decades — a pattern until now mainly seen in disease-causing pathogens. 'Our findings show that gut bacteria are also more dynamic than previously thought. Well-adapted strains can spread internationally and occupy new ecological niches,' said study leader Martin F. Polz of the University of Vienna. The team next plans to study which genes distinguish the identified populations and what biological functions those genes control.