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Microbial Ecology

RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

Gerald W. Tannock, Blair Lawley, Karen Munro, Ian M. Sims, Julian Lee, Christine A. Butts, Nicole Roy
G. T. Macfarlane, Editor
Gerald W. Tannock
aDepartment of Microbiology, University of Otago, Dunedin, New Zealand
bRiddet Centre of Research Excellence, Palmerston North, New Zealand
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Blair Lawley
aDepartment of Microbiology, University of Otago, Dunedin, New Zealand
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Karen Munro
aDepartment of Microbiology, University of Otago, Dunedin, New Zealand
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Ian M. Sims
cCallaghan Innovation, Wellington, New Zealand
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Julian Lee
dFood and Nutrition Science Group, New Zealand Institute of Plant and Food Research, Palmerston North, New Zealand
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Christine A. Butts
dFood and Nutrition Science Group, New Zealand Institute of Plant and Food Research, Palmerston North, New Zealand
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Nicole Roy
bRiddet Centre of Research Excellence, Palmerston North, New Zealand
eFood Nutrition and Health Team, Food and Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
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G. T. Macfarlane
Roles: Editor
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DOI: 10.1128/AEM.03799-13
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ABSTRACT

Knowledge 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. RNA was 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. RNA extracted 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.

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RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel
Gerald W. Tannock, Blair Lawley, Karen Munro, Ian M. Sims, Julian Lee, Christine A. Butts, Nicole Roy
Applied and Environmental Microbiology Mar 2014, 80 (7) 2240-2247; DOI: 10.1128/AEM.03799-13

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RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel
Gerald W. Tannock, Blair Lawley, Karen Munro, Ian M. Sims, Julian Lee, Christine A. Butts, Nicole Roy
Applied and Environmental Microbiology Mar 2014, 80 (7) 2240-2247; DOI: 10.1128/AEM.03799-13
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Print ISSN: 0099-2240; Online ISSN: 1098-5336