Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon

El Aidy, S., Derrien, M., Merrifield, C. A., Levenez, F., Doré, J., Boekschoten, M. V., Dekker, J., Holmes, E., Zoetendal, E. G., van Baarlen, P., Claus, S. P. & Kleerebezem, M., Apr-2013, In : The ISME journal. 7, 4, p. 743-755 13 p.

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  • Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon

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  • Sahar El Aidy
  • Muriel Derrien
  • Claire A Merrifield
  • Florence Levenez
  • Joël Doré
  • Mark V Boekschoten
  • Jan Dekker
  • Elaine Holmes
  • Erwin G Zoetendal
  • Peter van Baarlen
  • Sandrine P Claus
  • Michiel Kleerebezem

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.

Original languageEnglish
Pages (from-to)743-755
Number of pages13
JournalThe ISME journal
Issue number4
Publication statusPublished - Apr-2013
Externally publishedYes


  • Animals, Bacteria, Colon, Diet, Gene Expression Profiling, Germ-Free Life, Intestinal Mucosa, Male, Metabolomics, Metagenome, Mice, Mice, Inbred C57BL, Random Allocation, Symbiosis

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