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

FEMS Microbiol Ecol. 2007 Apr;60(1):126-35. doi: 10.1111/j.1574-6941.2007.00281.x. Epub 2007 Feb 22.


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-(13)C]-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 (13)C-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 (13)C-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.

Publication types

  • Evaluation Study

MeSH terms

  • Bacteria, Anaerobic / classification
  • Bacteria, Anaerobic / genetics
  • Bacteria, Anaerobic / metabolism
  • Carbon Isotopes / metabolism
  • Fermentation
  • Glucose / metabolism*
  • Gram-Positive Bacteria / classification*
  • Gram-Positive Bacteria / genetics
  • Gram-Positive Bacteria / metabolism
  • Humans
  • Intestine, Small / microbiology*
  • Isotope Labeling / methods
  • Magnetic Resonance Spectroscopy / methods*
  • Models, Biological*
  • Molecular Sequence Data
  • Peristalsis
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal, 16S / genetics*
  • Sequence Analysis, DNA


  • Carbon Isotopes
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Glucose

Associated data

  • GENBANK/AM234672
  • GENBANK/AM234673
  • GENBANK/AM234674
  • GENBANK/AM234675
  • GENBANK/AM234676
  • GENBANK/AM234677
  • GENBANK/AM234678
  • GENBANK/AM234679
  • GENBANK/AM234680
  • GENBANK/AM234681
  • GENBANK/AM234682
  • GENBANK/AM234683
  • GENBANK/AM234684
  • GENBANK/AM234685
  • GENBANK/AM234686
  • GENBANK/AM234687