Genomics

Dataset Information

162

The metabolic niche of a prominent sulfate-reducing human gut bacterium [2]


ABSTRACT: Sulfate-reducing bacteria (SRB) colonize the guts of ~50% of humans and produce H2S, a signaling molecule with numerous host effects. We used genome-wide transposon mutagenesis and insertion-site sequencing (INSeq), RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy USA adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial 9-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for utilizing ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. While genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage’s substrate utilization preferences, allowing consumption of more reduced carbon sources, and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients, and a framework for examining how individuals lacking D. piger differ from those that harbor it. Overall design: 114 samples total. Experiment 1:(E1) Evaluation of changes in an artificial gut community's structure as a result of dietary oscillation (HF/HS vdsLFHPP); Experiment 2 (E2) Evaluation of changes in an artificial gut community's structure over time as a result of changes in dietary sulfur; Experiment 3(E3) Evaluation of changes in an artificial gut community's structure as a result of D. piger co-colonization in mice fed a HF/HS diet supplemented with chondroitin sulfate.

INSTRUMENT(S): Illumina Genome Analyzer IIx (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Desulfovibrio piger GOR1; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)

SUBMITTER: Federico E Rey  

PROVIDER: GSE48807 | GEO | 2013-07-12

SECONDARY ACCESSION(S): PRJNA211823

REPOSITORIES: GEO

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Publications

Metabolic niche of a prominent sulfate-reducing human gut bacterium.

Rey Federico E FE   Gonzalez Mark D MD   Cheng Jiye J   Wu Meng M   Ahern Philip P PP   Gordon Jeffrey I JI  

Proceedings of the National Academy of Sciences of the United States of America 20130729 33


Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of  ...[more]

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