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BioMed Research International
Volume 2017 (2017), Article ID 1829685, 13 pages
https://doi.org/10.1155/2017/1829685
Research Article

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro

1Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany
2AgResearch Ltd, Grasslands Research Centre, Palmerston North 4442, New Zealand
3The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4442, New Zealand
4Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
5Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany

Correspondence should be addressed to Markus Egert; ed.negnawtruf-sh@trege.sukram

Received 14 November 2016; Revised 9 January 2017; Accepted 18 January 2017; Published 16 February 2017

Academic Editor: Clara G. de los Reyes-Gavilan

Copyright © 2017 Elena Herrmann et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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 revealed Allobaculum spp. 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 principal 13C-labeled fermentation products, and suggested that “cross-feeding” occurred in the system. RNA-SIP combined with metabolic profiling of 13C-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.