Gut bacteria evolving to digest new starches in UPFs among industrialized zones

Experts have discovered that gut bacteria rapidly evolve in response to diets, as observed in the case of ultra-processed foods (UFPs).

Researchers at the University of California, Los Angeles (UCLA), in the US, found that gene variants enabling the digestion of starches from UPFs have become prevalent in certain bacteria in industrialized regions.

Different species display distinct evolutionary pressures, with one gene in particular dating back to the 1960s. This gene is linked to digesting maltodextrin, made from cornstarch. 

The researchers suggest that since starches have been industrially produced for only a few decades, natural selection must play a powerful role in making these genes dominant quickly.

Industrialization is driving evolutionary differences

The publication in Nature reveals that bacterial evolution differs between industrialized and non-industrialized parts of the world.

The researchers found that the bacteria’s rapid evolution was due to their transfer of DNA from one strain to another, a process known as horizontal gene transfer. This is known to be the same process that enables antimicrobial resistance quickly, however, it has remained unknown in gut microbes.

“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,” says UCLA doctoral student and paper first author Richard Wolff. 

“What are the gut microbiomes in industrialized populations responding to? We’ve picked out one example with these starches, but there are likely many possibilities we haven’t grappled with yet.”

Unraveling DNA 

The researchers examined the genomes of approximately 30 species of gut bacteria globally.

Gut bacteria are rapidly evolving to digest starches from UPFs, underscoring how modern diets can reshape the human microbiome.Wolff and the corresponding author, Nandita Garud, UCLA professor of ecology and evolutionary biology, created a new statistic that pinpoints the locations where genes rose to high frequencies or were “swept” in these bacteria’s DNA.

The statistic identifies regions of similarity amid a diverse background that distinguish different strains of the same species.

“Different strains of Escherichia coli, for example, have diverged from each other as much as humans have diverged from chimps, yet we call them the same species,” Garud points out. 

“Despite this diversity, there are still shared fragments of DNA present in many hosts — a hidden thread connecting our microbiomes.”

A bacterial mystery?

Wolff says that it is not certain whether the gene linked to the digestion of maltodextrin is specialized for it or relevant for a broader class of starch derivatives. 

“There might be intermediate steps as the bacteria adapt to different starch sources. There are a lot of steps in between eating a diet full of cassava and breadfruit and a diet full of Hot Cheetos or something like that.”

Bacteria can acquire new DNA by consuming it, through an infected virus, or through horizontal gene transfer when bacteria clump together.

Since bacteria can absorb DNA from the environment through various methods, and humans harbor only some strains of the same species of gut bacteria that persist for many years, the researchers question: “How do DNA fragments become shared between individual humans?”

“Each person might have a couple of different strains of E. coli,” says Garud. “If fragments of DNA are transmitted horizontally across different strains in different hosts, and these strains seemingly are faithful to their respective hosts, where do they recombine? How do they move between individual people to become fixed in a whole population?”

The researchers believe the answer can be found in the future. However, their discovery of gut bacteria’s rapid evolution linked to diets, and that new starches add evolutionary pressure on them, calls for further caution regarding what foods we eat, as they play a larger role in promoting health than previously thought.

In related news, we examined the UPF debate where the ACI Group and Specialised Nutrition Europe argue that processing itself is not the problem; rather, its purpose and intensity determine health outcomes.