Title
Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing
Author
Egert, M.
de Graaf, A.A.
Maathuis, A.
de Waard, P.
Plugge, C.M.
Smidt, H.
Deutz, N.E.P.
Dijkema, C.
de Vos, W.M.
Venema, K.
TNO Kwaliteit van Leven
Publication year
2007
Abstract
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. © 2007 Federation of European Microbiological Societies.
Subject
Biology
Biomedical Research
Carbohydrates
Digestion
Metabolic profiling
NMR
Stable isotope probing
acetic acid
alcohol
bacterial RNA
butyric acid
carbohydrate
carbon 13
formic acid
glucose
glycerol
lactic acid
RNA 16S
stable isotope
bacterium
carbohydrate
digestion
fermentation
glucose
inoculation
microbial activity
phylogenetics
RNA
stable isotope
article
bacterium identification
Clostridium perfringens
controlled study
density gradient centrifugation
fermentation
gastrointestinal tract
in vitro study
inoculation
intestine
lactic acid bacterium
Lactobacillus fermentum
microflora
molecular phylogeny
molecular probe
nonhuman
nuclear magnetic resonance spectroscopy
nucleotide sequence
priority journal
RNA fingerprinting
RNA stability
strain difference
Streptococcus bovis
Bacteria, Anaerobic
Carbon Isotopes
Fermentation
Glucose
Gram-Positive Bacteria
Humans
Intestine, Small
Isotope Labeling
Magnetic Resonance Spectroscopy
Models, Biological
Molecular Sequence Data
Peristalsis
RNA, Bacterial
RNA, Ribosomal, 16S
Sequence Analysis, DNA
Bacteria (microorganisms)
Clostridium perfringens
Lactobacillus fermentum
Streptococcus bovis
To reference this document use:
http://resolver.tudelft.nl/uuid:b6c20028-d997-4bdf-a34b-81c6e83cc8c0
DOI
https://doi.org/10.1111/j.1574-6941.2007.00281.x
TNO identifier
239922
ISSN
0168-6496
Source
FEMS Microbiology Ecology, 60 (1), 126-135
Document type
article