title: Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon.
abstract: The interplay between dietary nutrients, gut microbiota and mammalian host tissues of the gastrointestinal tract is recognised as highly relevant for host health. Combined transcriptome, metabonome and microbial profiling tools were employed to analyse the dynamic responses of germfree mouse colonic mucosa to colonisation by normal mouse microbiota (conventionalisation) at different time-points during 16 days. The colonising microbiota showed a shift from early (days 1 and 2) to later colonisers (days 8 and 16). The dynamic changes in the microbial community were rapidly reflected by the urine metabolic profiles (day 1) and at later stages (day 4 onward) by the colon mucosa transcriptome and metabolic profiles. Correlations of host transcriptomes, metabolite patterns and microbiota composition revealed associations between Bacilli and Proteobacteria, and differential expression of host genes involved in energy and anabolic metabolism. Differential gene expression correlated with scyllo- and myo-inositol, glutamine, glycine and alanine levels in colonic tissues during the time span of conventionalisation. Our combined time-resolved analyses may help to expand the understanding of host-microbe molecular interactions during the microbial establishment.
authors.affiliation: Top Institute Food and Nutrition, Wageningen, Wageningen, The Netherlands.
authors.forename: Sahar
authors.initials: S
authors.lastname: El Aidy
authors.forename: Muriel
authors.initials: M
authors.lastname: Derrien
authors.forename: Claire A
authors.initials: CA
authors.lastname: Merrifield
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
authors.forename: Mark V
authors.initials: MV
authors.lastname: Boekschoten
authors.forename: Jan
authors.initials: J
authors.lastname: Dekker
authors.forename: Elaine
authors.initials: E
authors.lastname: Holmes
authors.forename: Erwin G
authors.initials: EG
authors.lastname: Zoetendal
authors.forename: Peter
authors.initials: P
authors.lastname: van Baarlen
authors.forename: Sandrine P
authors.initials: SP
authors.lastname: Claus
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000378:metabolism*; D003106:Colon / Q000378:metabolism / Q000382:microbiology*; D004032:Diet; D020869:Gene Expression Profiling; D005856:Germ-Free Life; D007413:Intestinal Mucosa / Q000382:microbiology*; D008297:Male; D055432:Metabolomics; D054892:Metagenome; D051379:Mice / Q000382:microbiology*; D008810:Mice, Inbred C57BL; D011897:Random Allocation; D013559:Symbiosis