Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans

Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber, but evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multi-enzymatic cellulosome systems capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut potentially during domestication, where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations, but are extremely rare in populations from industrialized societies, suggesting potential disappearance in response to the westernized lifestyle., , , # Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans

Data sources files for all figures and supplementary material

Description of the data and file structure

Data S1 Figure 1B tree.nwk is an unrooted phylogenetic tree, computed with the maximum likelihood method, of 62 selected genomes and MAGs, using the sequence of the ScaC scaffoldin as a phylotyping marker. The file contains the newick format used to create phylogenetic tree.

Data S2 Figure 1C data.xlsx Genomic dissimilarity computed by Mash distance within the novel identified ruminococcal cellulosomal species and pairwise comparisons to each other as well as to the ruminal R. flavefaciens species and the human species, R. champanellensis. Each column represents the mash distances.

Data S3 Figure 2A.xlsx, Observed collective prevalence of the MAGs for fiber-degrading strains in various human, apes and NHP cohorts. Values in columns represents the number of positive individuals, and percentages ar...