Synergy between Enterobacteriaceae and dietary components shapes the competition between the dominant anaerobes of the human gut
The human gut microbiota is frequently dominated by the Bacteroidota phylum, with Bacteroidaceae and Prevotellaceae families prevailing in modern and traditional lifestyles, respectively. While these distinct profiles have been well-documented across cohorts, the underlying mechanisms remain poorly understood. Here, we combine defined gut community models and genetic tools to experimentally dissect the ecological principles that favor Prevotellaceae or Bacteroidaceae. Testing 94 dietary components in the community model shows these two families compete for overlapping nutritional niches. Notably, Segatella copri, a key Prevotellaceae representative, outcompetes Bacteroidaceae strains when preferred polysaccharides are available. Interestingly, this competitive advantage depends on the presence of Enterobacteriaceae, which synergize with dietary components to promote Segatella dominance. Accordingly, we observe that global Segatella-rich non-Westernized microbiomes correlate with higher Enterobacteriaceae content. Our results suggest a revised hypothesis in which the ecosystem-level dynamic interplay between dietary components and key commensals within the community contributes to distinct Bacteroidota family dominance.