What we eat doesn’t just affect our bodies — it also shapes the evolution of the trillions of microbes living inside us.
A new study from UCLA shows that gut bacteria have evolved remarkably fast to digest starches found in ultra-processed foods, revealing how modern diets are reshaping our microbiomes in real time.
In research published in Nature, evolutionary biologists analyzed the genomes of nearly three dozen common gut bacteria species using data from people around the world.
They found that in industrialized countries, certain genes that help bacteria break down industrially produced starches have rapidly become dominant.
These starches, such as maltodextrin, have only been widely used in foods since the 1960s, meaning the changes must have occurred within just a few decades — an eye-blink in evolutionary terms.
The scientists concluded that strong natural selection is driving this rapid shift. Bacteria that can efficiently digest these new food ingredients gain an advantage and spread quickly through populations.
Even more striking, the study found clear differences between gut bacteria in industrialized and non-industrialized societies. Different genes appear to be favored depending on diet, suggesting that microbiomes are adapting in distinct ways based on how people eat around the world.
To uncover this pattern, the researchers developed a new method to detect “selective sweeps” — regions of DNA that suddenly become very common within a species.
This is challenging because strains of the same bacterial species can be incredibly different from one another. In fact, the genetic differences between strains of E. coli can be as large as the differences between humans and chimpanzees.
Despite this diversity, the team identified small shared DNA fragments that appear repeatedly across many individuals, pointing to strong evolutionary pressure.
One gene stood out in particular. It is associated with digesting maltodextrin, a starch derived from corn and commonly added to processed foods for texture and shelf stability. This gene was sweeping through gut bacteria only in industrialized populations, not in people eating more traditional diets.
The researchers caution that maltodextrin may be just one example. Bacteria could be adapting to a broader range of modern starches and additives found in processed foods.
The shift from traditional diets based on whole plants to diets heavy in packaged snacks and refined ingredients likely presents many new challenges and opportunities for gut microbes.
The study also highlighted the role of horizontal gene transfer — a process in which bacteria share DNA directly with one another rather than passing it down through generations. This mechanism is already known for spreading antibiotic resistance, but this research shows it also allows gut bacteria to adapt rapidly to dietary change.
One puzzle remains unanswered: how these genes spread so widely between people, given that individuals typically carry their own stable strains of bacteria for years. Understanding how bacteria exchange genes across hosts will be an important focus of future research.
Overall, the findings suggest that modern diets may be influencing human health in deeper and more complex ways than previously thought, not only by affecting our bodies directly but by actively steering the evolution of our gut microbes.
