Identification of glucose-fermenting bacteria present in an in-vitro model of the human inetstine by RNA-stable isotope probing

M.G.G. Egert, A.A. de Graaf, A. Maathuis, P. de Waard, C.M. Plugge, H. Smidt, N.E.P. Deutz, C. Dijkema, W.M. de Vos, K. Venema

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16S rRNA-based stable isotope probing (SIP) and nuclear magnetic resonance (NMR) spectroscopy-based metabolic profiling were used to identify bacteria fermenting glucose under conditions simulating the human intestine. The TIM-2 in vitro model of the human intestine was inoculated with a GI tract microbiota resembling that of the small intestine, to which subsequently 4, 20 or 40 mM of [U-13C]-glucose were added. RNA was extracted from lumen samples after 0 (control), 1, 2 and 4 h and subjected to density-gradient ultracentrifugation. Phylogenetic analysis of unlabeled 16S rRNA revealed a microbial community dominated by lactic acid bacteria and Clostridium perfringens. Distinct 13C-incorporation into bacterial RNA was only observed for the 40-mM addition. 16S rRNA fingerprinting showed an activity drop of Lactobacillus fermentum after glucose addition, while Streptococcus bovis and C. perfringens were identified as the most active glucose-fermenters. Accordingly, NMR analysis identified lactate, acetate, butyrate and formate as the principal fermentation products, constituting up to 91% of the 13C-carbon balance. RNA-SIP combined with metabolic profiling allowed us to detect differential utilization of a general model carbohydrate, indicating that this approach holds great potential to identify bacteria involved in the fermentation of dietary relevant oligo- and polymeric carbohydrates in the human intestine.
Original languageEnglish
Pages (from-to)126-135
JournalFEMS Microbiology Ecology
Issue number1
Publication statusPublished - 2007


  • microbial community structure
  • fragment-length-polymorphism
  • chain fatty-acids
  • propionate oxidation
  • diversity
  • pcr
  • microorganisms
  • tract
  • colon
  • bias


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