Title
Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing
Author
Kovatcheva-Datchary, P.
Egert, M.
Maathuis, A.
Rajilić-Stojanović, M.
de Graaf, A.A.
Smidt, H.
de Vos, W.M.
Venema, K.
TNO Kwaliteit van Leven
Publication year
2009
Abstract
Summary Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l-1 of [U-13C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain. © 2008 The Authors. Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd.
Subject
Biology
biomedical research
acetic acid derivative
bacterial DNA
bacterial RNA
butyric acid derivative
isotope
propionic acid derivative
ribosome DNA
RNA 16S
starch
article
bacterium
chemistry
classification
DNA fingerprinting
DNA sequence
fermentation
genetics
growth, development and aging
human
in vitro study
large intestine
metabolism
microbiology
molecular genetics
nucleotide sequence
phylogeny
restriction fragment length polymorphism
RNA gene
sequence homology
staining
Acetates
Bacteria
Butyrates
DNA Fingerprinting
DNA, Bacterial
DNA, Ribosomal
fermentation
genes, rRNA
humans
large intestine
isotopes
molecular sequence data
phylogeny
polymorphism
restriction fragment length
propionates
bacterial RNA
ribosomal RNA 16S
sequence analysis DNA
sequence homology
nucleic acid
staining and labeling
starch
bacteria (microorganisms)
bifidobacterium adolescentis
eubacterium rectale
prevotella
ruminococcus
ruminococcus bromii
To reference this document use:
http://resolver.tudelft.nl/uuid:079fff8f-dfb9-4b1c-984b-962e1183cacc
DOI
https://doi.org/10.1111/j.1462-2920.2008.01815.x
TNO identifier
241464
ISSN
1462-2912
Source
Environmental Microbiology, 11 (4), 914-926
Document type
article