Humans Are Losing Key Microbes That Turn Fiber Into Food

City-living humans are losing vital bacterial allies, according to new research.

After comparing the gut microbes of people living in industrial, rural and hunter-gatherer societies, researchers in Israel discovered that the more urbanized the person, the less cellulose-degrading bacteria found in their gut.

This microbial loss has worrying implications, as cellulose-degrading bacteria are needed to digest the fiber found in fruits and vegetables.

The findings were published in Science.

Gutted

After gathering microbial samples from participants, the researchers from the Ben-Gurion University of the Negev and the Weizmann Institute of Science, Israel, analyzed the genomes of the bacteria, searching for the key genes involved in the breakdown of cellulose – a key component of plant cell walls.

“It’s no easy task to degrade cellulose, few bacteria can do it,” said Edward Bayer, a professor at the Weizmann Institute. Bayer is an expert on cellulosomes – multi-enzyme complexes that are able to degrade plant cell walls. “Cellulose is difficult to digest because it is insoluble. Fiber in the gut is like a tree-trunk in a swimming pool, it gets wet, but it does not dissolve.”

Bayer and his colleagues discovered previously unknown bacterial species, provisionally named Ruminococcus primaciens, Ruminococcus hominiciens and Ruminococcus ruminiciens, all of which form functional multi-enzymatic systems that degrade crystalline cellulose.

The first of these species, R. primaciens, is more present in nonhuman primates and hunter-gatherer human populations like the Hadza of Tanzania, while R. hominiciens is more present in the guts of rural and city-dwelling humans and great apes.

Analysis by the research team suggests that, rather than R. hominiciens being an offshoot of R. primaciens, the former bacterium is likely an immigrant species from the ruminant gut, possibly migrating from the digestive tracts of cows during the agricultural revolution.

“We were surprised to see that the cellulosome-producing bacteria of humans seem to have switched hosts during evolution, because the strains from humans are more closely related to the strains from livestock than to the strains from our own primate ancestors,” said Itzhak Mizrahi, a professor of microbial evolution at Ben-Gurion University of the Negev.

Despite originating from grass-grinding guts, however, R. hominiciens doesn’t seem to be helping city-living humans digest cellulose very much, given how little of the bacterium is present in industrialized humans.

The authors of the paper posit that Western diets of processed foods and few vegetables have altered the microbe-makeup of industrialized humans, eliminating much of the R. hominiciens that would otherwise cohabit in people’s guts.

“Our ancestors in Africa 200,000 years ago did not pick up lunch from a drive-through, or phone in a home-delivery for dinner,” remarked William Martin, a professor of evolutionary biology at the Heinrich Heine University Düsseldorf and coauthor of the study.

Reference: Moraïs S, Winkler S, Zorea A, et al. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science. 2024;383(6688):eadj9223. doi: 10.1126/science.adj9223

This article is a rework of a press release issued by Ben-Gurion University of the Negev. Material has been edited for length and content.