Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

Park, Sun-Yang; Rao, Chitong; Coyte, Katharine Z.; Kuziel, Gavin A.; Zhang, Yancong; Huang, Wentao; Franzosa, Eric A.; Weng, Jing‐Ke; Huttenhower, Curtis; Rakoff-Nahoum, Seth

doi:10.1016/j.cell.2022.01.002

Cited by 51 publications

(35 citation statements)

References 81 publications

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“…The authors observed similar preferences for carbohydrate sources among closely related species, along with paradoxically high diversity in PUL distribution. Their findings complement the discovery by Park et al that Bacteroides fitness is, in part, determined by context-dependent inhibition by the metabolite butyrate, depending on the specific sugars utilized by individual strains ( 16 ). Integrating these groups’ data sets could even further inform our understanding of carbohydrate utilization and its evolution in the intestine.…”

Section: Commentarysupporting

confidence: 75%

Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota

Fansler

Zhu

2022

mSystems

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Section: Commentarysupporting

confidence: 75%

Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota

Fansler

Zhu

2022

mSystems

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“…Acyl-CoA transferases like the AarC enzyme appear to be more generally involved in differentiating important metabolic roles of closely related bacteria in the microbiome. A recent comprehensive study of Bacteroidetes in the human microbiome uncovered a trade-off similar to the one described here that involves acyl-CoA transferases acting on butyrate 39 . This has the exciting implication that there may be generalizable trade-offs involving acyl-CoA transferases that act on SCFAs.…”

Section: Discussionmentioning

confidence: 61%

Differential partitioning of key carbon substrates at the rumen wall by recently diverged Campylobacteraceae populations

Strachan

Neubauer

et al. 2022

Preprint

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While the activities of different microbes in the rumen have been shown to modulate the host’s ability to utilize plant biomass, microbes colonizing the host-rumen interface have received little attention. Here, we show that highly abundant Campylobacteraceae on the rumen epithelia have recently diverged into two populations, one of which has become a sink for acetate, the main carbon source for the host. Genomic comparisons suggest that the populations were structured by genome-wide selective sweeps after which they acquired several specific adaptations. These include differential expression and domain duplication in acetate utilization genes, which led to the ability to grow on acetate but also to inhibition by propionate in one population. This metabolic trade-off also manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture independent analyses, our results highlight recent evolutionary dynamics with unexpected consequences for ruminant nutrition.

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“…Although the microbiota’s metabolic output dramatically affects the gut ecosystem, the metabolic input of each species also shapes its interactions with other microbes and the host (Coyte and Rakoff-Nahoum, 2019; Park et al, 2022; Tuncil et al, 2017). Plant polysaccharides that are undigested by host enzymes in the proximal intestine, such as dietary fibers, are the most commonly utilized carbon source by the microbiota, and collectively these glycans are termed dietary Microbiota Accessible Carbohydrates (MACs) (Porter, Nathan T and Martens, Eric C, 2017; Sonnenburg and Sonnenburg, 2014; Wardman et al, 2022).…”

Section: Resultsmentioning

confidence: 99%

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition

Gerrick

West

Mechler

et al. 2022

Preprint

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Protists in the gut microbiota influence intestinal immunity and epithelial composition, yet the mechanisms used by these protists to shape the gut environment remain poorly understood. Here, we identify a new protist species, Tritrichomonas casperi, and show that metabolic differences between closely related commensal protists modulate their effects on host immunity and determine their ecological niche within the murine microbiota. Genomic and metabolomic analysis of commensal tritrichomonads reveal species-level differences in excretion of the tuft cell activating metabolite succinate, leading to differential induction of Th1, Th2, and Th17 cells in the small intestine. Using defined diets and in vitro growth assays, we show that different tritrichomonad species preferentially rely on dietary polysaccharides or mucus glycans, which leads to trans-kingdom competition with specific bacteria in the microbiota. Our findings elucidate differences in commensal tritrichomonad metabolism and suggest how dietary interventions could regulate the impact of these protists on gut health.

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Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

Cited by 51 publications

References 81 publications

Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota

Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota

Differential partitioning of key carbon substrates at the rumen wall by recently diverged Campylobacteraceae populations

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition

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