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TitleRNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel
Publication TypeJournal Article
Year of Publication2014
AuthorsTannock, G.W., Lawley B., Munro K., Sims I.M., Lee J., Butts C.A., and Roy N.
JournalApplied and Environmental Microbiology
Pagination2240 - 2247
Date Published2014
ISSN00992240 (ISSN)
Keywords16S rRNA gene, Animal, Animals, article, Bacteria, Bacterial cells, bacterial DNA, Bacterial population, Bacterial species, bacterium, Bifidobacterium animalis, biology, Buoyancy, Buoyant density, carbon, chemistry, diet, DNA sequence, DNA, Bacterial, DNA, Ribosomal, genetics, growth rate, Hydrolysis products, Intestine, Large, inulin, isolation and purification, isotope labeling, Isotopes, large intestine, metabolism, microbiology, molecular genetics, Molecular Sequence Data, nucleic acid, Nutrition, phylogeny, Polysaccharides, rat, Rats, ribosome DNA, RNA, RNA 16S, RNA, Ribosomal, 16S, Sequence Analysis, DNA, stable isotope, Stable isotopes, substrate, Substrates
AbstractKnowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (13C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin- derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [13C]inulin diet.RNAwas extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect 13C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent.RNAextracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the 13C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism. © 2014, American Society for Microbiology.

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