title: RNA-Based Stable Isotope Probing SuggestsAllobaculumspp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro.
abstract: RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria in a complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic conditions for 0, 2, and 4 h with 40 mM [U13C]glucose. Isopycnic density gradient ultracentrifugation and fractionation of isolated RNA into labeled and unlabeled fractions followed by 16S rRNA sequencing showed a quick adaptation of the bacterial community in response to the added sugar, which was dominated by unclassified Lachnospiraceae species. Inspection of distinct fractions of isotope-labeled RNA revealedAllobaculumspp. as particularly active glucose utilizers in the system, as the corresponding RNA showed significantly higher proportions among the labeled RNA. With time, the labeled sugar was used by a wider spectrum of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U13C]glucose, with lactate, acetate, and propionate being the principal13C-labeled fermentation products, and suggested that "cross-feeding" occurred in the system. RNA-SIP combined with metabolic profiling of13C-labeled products allowed insights into the microbial assimilation of a general model substrate, demonstrating the appropriateness of this technology to study assimilation processes of nutritionally more relevant substrates, for example, prebiotic carbohydrates, in the gut microbiota of mice as a model system.
authors.affiliation: Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany.
authors.forename: Elena
authors.initials: E
authors.lastname: Herrmann
authors.affiliation: AgResearch Ltd, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Wayne
authors.initials: W
authors.lastname: Young
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4442, New Zealand.
authors.forename: Douglas
authors.initials: D
authors.lastname: Rosendale
authors.affiliation: Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany.
authors.forename: Verena
authors.initials: V
authors.lastname: Reichert-Grimm
authors.affiliation: Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany.
authors.forename: Christian U
authors.identifier: 0000-0001-7134-7085
authors.initials: CU
authors.lastname: Riedel
authors.affiliation: Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Conrad
authors.affiliation: Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany.
authors.forename: Markus
authors.identifier: 0000-0003-2402-3322
authors.initials: M
authors.lastname: Egert
mesh_terms: D000818:Animals; D002247:Carbon Isotopes / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid; D018076:DNA, Complementary / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D005285:Fermentation; D000068536:Bacillota / Q000235:genetics / Q000378:metabolism*; D000069196:Gastrointestinal Microbiome; D005947:Glucose / Q000378:metabolism*; D007553:Isotope Labeling; D051379:Mice; D008810:Mice, Inbred C57BL; D010802:Phylogeny; D025341:Principal Component Analysis; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D002247:Carbon Isotopes; D018076:DNA, Complementary; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D005947:Glucose