Human gut bacteria genome is directly impacted by industrialization
Phylogenetic methods built to trace evolution over billions of years find that gut bacteria in industrialized societies have more and different genes, which might influence human health
From regulating our metabolism and immune defense to influencing our hormonal and neurological pathways via the gut-brain axis, our gut microbiome has been found to serve more and more roles pivotal to our health.
The bacteria in our guts inhabit very different worlds depending on how we live. Diet, sanitation and medication all differ between industrialized and non-industrialized societies, and we have known for some time that these factors change which bacteria are present. But do our symbiotic bacteria evolve in response to our evolving lifestyle?
A new study published in Cell has now shown that the answer appears to be yes, and in parallel across different species of bacteria, finding that strains from industrialized hosts carry more genes, which were gained recently, mostly from other microbes. The study also found signs of selection in the same kinds of functions across different species, including stress response, remodeling of the cell envelope, and central metabolism. These include genes for making vitamin B12, and genes for making lipopolysaccharide, a component of the bacterial surface that our immune system recognizes, which may have consequences for human health that remain to be explored.
The study was led by researchers from Kiel University and MIT, with evolutionary modelling by researchers from the Model-Based Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology (OIST), headed by Professor Gergely Szöllősi.
“It's always exciting when the methods and tools we develop to answer deep evolutionary questions can be repurposed to datasets and questions closer to the present that may have a more direct impact on our everyday life. Understanding how the bugs in our guts pick up new genes is a good example for this. I hope our results will inspire further studies to use this knowledge in supporting us to live a healthier life in our changing environment,” says Lénárd Szánthó, a senior bioinformatician in the OIST unit.
From deep past to modern history
The multinational team focused on ten bacterial species that were well-sampled in both industrialized and non-industrialized hosts. In all ten, strains from industrialized hosts had larger sets of protein-coding genes, a difference that was statistically significant in eight, and strains within a species differed more from one another in gene content.
Larger genomes could mean two very different things. The strains may have gained the genes recently, or their ancestors may already have had them, and industrial environments simply favored those strains. Telling these explanations apart is where the OIST contribution comes in. Phylogenetic reconciliation compares the family tree of each gene with the family tree of the species that carries it, and any mismatches between the trees reveal where genes were gained, lost, or transferred. The OIST group developed these methods to study the deep past, including the early evolution of bacteria and the origin of fungi, on time scales of hundreds of millions and billions of years. Now, Szánthó has modified them to the relatively recent history of the gut microbiome as it adapts to industrialization.
The results were clear: gene gains were concentrated on the tips of the trees (i.e. in recent evolution) and were higher along branches associated with industrialized hosts. Between 80% and 90% of the gains were horizontal gene transfers, in which bacteria take up genes from other microbes rather than inheriting them from their parents, often together with mobile elements such as plasmids and phages.
"These methods were built to look back hundreds of millions and billions of years, so it was not obvious that they would tell us anything about something this recent," said Szöllősi. "Lénárd made them work for this problem, and the picture that comes out is that bacteria in industrialized hosts have been acquiring genes from their neighbors recently, and this is what makes their genomes larger."
The authors are careful about what the data cannot show. It is still unclear which aspect of industrial life, whether diet, medication, sanitation, or something else, is responsible for these patterns. It is also not settled that the larger genomes are themselves an adaptation, since they may partly reflect weaker selection against extra genes. And the analysis covers ten species, so whether the patterns hold more widely will need further work.
The team worked with cultured bacteria as well as with DNA reconstructed from stool samples. They added 1,841 new genomes to the collection of the Global Microbiome Conservancy, and used a further 4,140 data samples from the collection for a total of 5,981 isolate genomes from 56 donors in 9 countries. The Global Microbiome Conservancy is an international initiative that works with communities around the world, with a particular emphasis on populations underrepresented in microbiome research, and is building an open, non-profit library of human gut bacteria.
Journal
Cell
Method of Research
Data/statistical analysis
Subject of Research
Cells
Article Title
Convergent genomic evolution of human gut bacteria along an industrialization gradient
Article Publication Date
2-Nov-2026
COI Statement
R.J.X. is a co-founder of Convergence Bio, a board director at MoonLake Immunotherapeutics, a consultant to Nestlé, and a member of the advisory boards at Magnet Biomedicine and Arena Bioworks. None of the organizations listed above provided funding for this study.
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