The gut microbiome is complex, and can be affected by the things we eat, our physical habits, our genes, and other factors. New research has shown that the gut microbiome can also evolve rapidly when exposed to different diets. Scientists determined that when gut microbes were exposed to starchy, ultra-processed foods, genetic changes arose that helped the microbes digest a processed ingredient in the food–maltodextrin. This process may have led to significant shifts in the genomes of some gut microbes that are found in people who live in industrialized nations. The study also determined that gut microbes are evolving in different ways in different parts of the world, depending on whether they are industrialized or not.
The starches that are often found in ultra-processed foods are synthetic, and have only existed for a few decades. So the researchers suspect that a natural selection effect must have rapidly boosted certain genes and genetic changes that can aid in the digestion of these foods. The findings have been reported in Nature.
In this work, the investigators analyzed the genomes of over 30 species of gut microbes. Bacteria can easily share genes with one another in a process known as horizontal gene transfer. This study revealed that horizontal gene transfer is helping gut microbes evolve quickly.
"The discovery that the ability to digest novel starches is a target of natural selection in gut bacteria is interesting, but we found an even more robust, stronger signal that there are different targets of selection across many genes and many species in industrialized and non-industrialized populations," said first study author Richard Wolff, a graduate student at UCLA.
"What are the gut microbiomes in industrialized populations responding to? We've picked out one example with these starches, but there's likely many possibilities we haven't grappled with yet."
The scientists created a way to identify the places in the genomes of gut bacteria that are common and can be found frequently; these genetic regions are very similar compared to the vast diversity among the genomes of gut microbes.
"Different strains of E. coli, for example, have diverged from each other as much as humans have diverged from chimps, yet we call them the same species. Despite this diversity, there are still shared fragments of DNA present in many hosts—a hidden thread connecting our microbiomes," explained corresponding study author Nandita Garud, a UCLA professor of ecology and evolutionary biology.
There were different microbial genes that were selected for in industrialized nations compared to non-industrialized nations. One gene stood out in industrialized areas: a bacterial gene that aids in maltodextrin digestion. Maltodextrin is a synthetic additive that has been used in processed foods for about six decades.
"We saw the adaptive signal very strongly, but we can't say for sure yet if it's specializing in maltodextrin or a broader class of starch derivatives. There might be intermediate steps as the bacteria adapt to different starch sources," said Wolff. “There are a lot of steps between eating a diet full of cassava and breadfruit and a diet full of hot Cheetos or something like that."
Now the investigators are interested in learning more about how gut bacteria evolve from one human to another; not just within the same person.
For now, the research has shown what a dramatic effect diet can have on gut microbes, and that the right diet could have an even more significant role in boosting good health than we knew, while the opposite may also be true.
Sources: University of California Los Angeles (UCLA), Nature
