Maintenance of diversity in host-associated and engineered microbial communities is essential to stable division of metabolic labor across multiple interacting organisms, but the mechanisms that maintain it are poorly understood. Loss of microbial diversity frequently results in reductions in community performance; in the human gut microbiome, low diversity is linked to multiple acute and chronic disease states, such as metabolic syndrome, type 2 diabetes, inflammatory bowel diseases, and colorectal cancer. Human consumption of dietary fibers, which are polysaccharides that are not degraded by human enzymes but are fermented by gut microbiota, is thought to maintain gut microbiome diversity in this ecosystem. However, it remains unclear to what degree generalizable features of highly-diverse polysaccharide chemical structures allow the non-competitive maintenance of diversity, presumably by allowing microbial specialization in consumption of specific structural motifs. Here we tested the hypotheses 1) that very fine structural differences govern the outcome of microbial oligo/polysaccharide fermentation, and 2) that these fine structural differences compound over generations, resulting in niche partitioning among degrading microbiota and, therefore, cooperative degradation. We tested these hypotheses through <i>in vitro </i>fermentation of polysaccharides with varying structures as sole carbon substrates by human fecal microbiota over sequential generations of selection and measured alterations in microbial community structure (via 16S amplicon sequencing) and metabolic outcome (e.g. short-chain fatty acids). We found that 1) very fine differences in hemicellulose structures generated divergent fermentation outcomes, both in microbial species composition and metabolic fate, 2) that consumption of complex carbohydrates resulted in stable fermenting communities over sequential transfers, 3) that very similar consortia were selected in fermentation of the same polysaccharide across multiple donors with divergent initial microbiota, 4) that species were specific to polysaccharide structures, and 5) that the competition was resolved at the level of individual genotypes (“strains”) of species. Taken together, these data suggest that the carbohydrate structures generate distinct niches and, therefore, maintain microbial diversity, suggesting that rational design of carbohydrate-microbiota interactions may be employed for stable division of labor in bioprocesses.   <br/>

Fine carbohydrate structure sustains diversity in microbial consortia and governs competition at the strain level

2019 Spring National Meeting

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