E-GEOD-14737 - Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

Status
Submitted on 6 February 2009, released on 22 May 2010, last updated on 27 March 2012
Organism
Bacteroides thetaiotaomicron, Eubacterium rectale
Samples (16)
Array (1)
Protocols (7)
Description
The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability. The interactions between E. rectale and B. thetaiotaomicron were characterized by performing whole genome transcriptional profiling of each species after colonization of gnotobiotic mice with each organism alone, or in combination. E. rectale was also profiled during in vitro growth.
Experiment type
transcription profiling by array 
Contacts
Federico E Rey <reyf@wustl.edu>, Henning Seedorf, Jeffrey I Gorodn, Michael A Mahowald, Peter J Turnbaugh
Citation
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-14737.idf.txt
Sample and data relationshipE-GEOD-14737.sdrf.txt
Raw data (1)E-GEOD-14737.raw.1.zip
Processed data (1)E-GEOD-14737.processed.1.zip
Array designA-GEOD-7006.adf.txt
R ExpressionSetE-GEOD-14737.eSet.r
Links