|
| Status |
Public on Jun 29, 2013 |
| Title |
The metabolic niche of a prominent sulfate-reducing human gut bacterium [1] |
| Organisms |
[Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Collinsella aerofaciens ATCC 25986; Marvinbryantia formatexigens DSM 14469; Escherichia coli str. K-12 substr. MG1655; Agathobacter rectalis ATCC 33656; Desulfovibrio piger GOR1 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| |
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| Overall design |
mRNA profiles of fecal contents from gnotobiotic mice colonized with defined consortia of human gut associated microbes
|
| |
|
| Contributor(s) |
Rey F, Gordon JI |
| Citation(s) |
23898195 |
| |
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico E Rey |
| E-mail(s) |
reyf@wustl.edu
|
| Phone |
314-963-0284
|
| Organization name |
Washington University
|
| Department |
Pathology
|
| Lab |
Gordon
|
| Street address |
4444 Forest Park Blvd
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17383 |
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) |
|
| Samples (13)
|
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| This SubSeries is part of SuperSeries: |
| GSE48809 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium |
|
| Relations |
| BioProject |
PRJNA209979 |
| SRA |
SRP026386 |
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