title: Impact of commensal microbiota on murine gastrointestinal tract gene ontologies.
abstract: The gastrointestinal tract (GIT) of eukaryotes is colonized by a vast number of bacteria, where the commensal microbiota play an important role in defining the healthy gut. To investigate the influence of commensal bacteria on multiple regions of the host GIT transcriptome, the gene expression profiles of the corpus, jejunum, descending colon, and rectum of conventional (n = 3) and germ-free mice (n = 3) were examined using the Affymetrix Mu74Av2 GeneChip. Differentially regulated genes were identified using the global error assessment model, and a novel method of Gene Ontology (GO) clustering was used to identify significantly modulated biological functions. The microbiota modify the greatest number of genes in the jejunum (267 genes with an alpha < 0.001) and the fewest in the rectum (137 genes with an alpha < 0.001). Clustering genes by GO biological process and molecular function annotations revealed that, despite the large number of differentially regulated genes, the residential microbiota most significantly modified genes involved in such biological processes as immune function and water transport all along the length of the mouse GIT. Additionally, region-specific communication between the host and microbiota were identified in the corpus and jejunum, where tissue kallikrein and apoptosis regulator activities were modulated, respectively. These findings identify important interactions between the microbiota and the mouse gut tissue transcriptome and, furthermore, suggest that interactions between the microbial population and host GIT are implicated in the coordination of region-specific functions.
authors.affiliation: Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland.
authors.forename: David M
authors.initials: DM
authors.lastname: Mutch
authors.forename: Rainer
authors.initials: R
authors.lastname: Simmering
authors.forename: Dominique
authors.initials: D
authors.lastname: Donnicola
authors.forename: Grigorios
authors.initials: G
authors.lastname: Fotopoulos
authors.forename: James A
authors.initials: JA
authors.lastname: Holzwarth
authors.forename: Gary
authors.initials: G
authors.lastname: Williamson
authors.forename: Irène
authors.initials: I
authors.lastname: Corthésy-Theulaz
mesh_terms: D000818:Animals; D041981:Gastrointestinal Tract / Q000378:metabolism* / Q000382:microbiology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics*; D005856:Germ-Free Life; D006262:Health; D007413:Intestinal Mucosa / Q000378:metabolism; D007422:Intestines / Q000382:microbiology; D051379:Mice; D008809:Mice, Inbred C3H; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D013559:Symbiosis / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D012333:RNA, Messenger