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Study Reveals History, Distribution of Plant-Degrading Microbes in the Human Gut

NEW YORK – While retracing the human acquisition of gut microbes capable of breaking down the tough plant compound cellulose, a team from Israel, Germany, the UK, and the US documented a decline in such cellulose-degrading gut bugs in individuals from industrialized populations, as compared to ancient humans, hunter-gatherers, and present-day, nonindustrialized populations.

In a study appearing in Science on Thursday, the researchers scrutinized tens of thousands of microbial genomes found within gut metagenomic sequences from ancient and modern-day humans from industrialized and nonindustrialized populations around the world, comparing them to one another and to the gut microbiomes of nonhuman primates and other animals, to search for cellulose-digesting "ruminococcal" bacteria.

"Our study significantly advances our understanding of the microbiome's role in cellulose digestion in the human gut, introducing insights into gut microbiome complexity and its evolutionary dynamics," senior and corresponding author Itzhak Mizrahi, a biotechnology, life sciences, and sustainability and climate change researcher at Ben-Gurion University of the Negev, said in an email.

Along the way, the team flagged a handful of previously unappreciated gut microbial species containing cellulosome machinery contributing to cellulolytic processes in the gut, Mizrahi explained, while also highlighting the evolutionary, environmental, and genetic processes that helped humans acquire such gut microbes — from the role of domestic ruminant animals in passing ancestral versions of the microbes to humans to the bacterial adaptations to the primate gut that were aided by horizontal gene transfer.

By searching 92,143 human metagenome-associated genomes (MAGs) and more than 4,900 rumen MAGs from domestic ruminant cattle for the ScaC gene that is found specifically in Ruminococcus genus bacteria, the team narrowed in on genomes belonging to such ruminococcal bacteria in the human and ruminant animal gut.

The set included three new cellulosome-containing ruminococcal species in the human gut, the researchers reported: Candidatus Ruminococcus hominiciensR. primaciens, and R. ruminiciens.

With follow-up phylogenetic and evolutionary analyses, they found that the R. primaciens species most closely resembled the proposed shared common ancestor of the cellulose-degrading ruminococcal strains currently found in human gut microbiomes.

The team further saw signs that at least one of these species, R. hominiciens, was found in the gut microbiome of ruminant animals before it moved to humans, likely due to increased human-ruminant interactions following animal domestication.

Although the strains appeared to rely on horizontal gene transfer to effectively adapt to the guts of humans and other primates, Mizrahi noted, the results also pointed to ongoing human acquisition of the cellulose-degrading microbes, which have continued to colonize and adapt to the human gut.

Nevertheless, the investigators described a decline in ruminococcal lineages in industrialized human populations, as compared to their gut abundance in Paleolithic humans, Hadza hunter-gatherers, rural communities, and nonindustrialized populations, potentially owing to dietary changes that tend to accompany industrialization.

But that also suggested to the researchers that there may be opportunities to boost the representation of cellulose-degrading ruminococcal microbes in the human gut to increase individuals' ability to obtain nutrients from plant-based food sources.

"The role of these microbes in the ancestral human gut hints at potential health implications due to shifts away from traditional diets, guiding public health strategies towards supporting a diverse and functional gut microbiome," Mizrahi said.

"These microbes can offer significant nutritional benefits, especially in resource-limited societies, by maximizing nutrition from plant fibers," he added, noting that there is "potential for their reintroduction into industrialized guts through diet and probiotics."