Subtle Differences in Fine Polysaccharide Structures Govern Selection and Succession of Human Gut Microbiota

Abstract

Dietary fibers are fermented in the human gut and are known to modulate microbiome composition and metabolic function, but few studies have explored to what extent the small variations in complex fiber structures impact community assembly, microbial division of labor, and organismal metabolic responses across individual microbiome structures. To test the hypothesis that subtle linkage variations in chemical structures of polysaccharides afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fermentation with fecal inocula from individual donors and measured microbial responses using an integrated multi-omics approach. We fermented two sorghum arabinoxylans (SAXs) as model complex polysaccharides, with fecal microbiota from three donors and an artificially high diversity mix of all three. Although differences in sugar linkage profiles across SAXs were subtle, surprisingly, consortia fermenting different AXs revealed distinct species-level genomic diversity and metabolic outcomes with nearly-identical strains on each polysaccharide across inocula. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials; however, CAZyme genes enriched in different AX-fermenting consortia were specific to SAX type and displayed various catabolic domain fusions with diverse accessory motifs, suggesting they may be functionally degenerate and this degeneracy may relate to fine substrate structure. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia, which are present amongst unrelated individuals.