Hindawi BioMed Research International Volume 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 Elena Herrmann,1 Wayne Young,2 Douglas Rosendale,3 Verena Reichert-Grimm,4 Christian U. Riedel,4 Ralf Conrad,5 and Markus Egert1 1 Institute 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; [email protected] 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. RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria ina complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic 13 conditionsfor0,2,and4hwith40mM[U C]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 13 of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U C]glucose, with lactate, acetate, and propionate being 13 the principal C-labeled fermentation products, and suggested that “cross-feeding” occurred in the system. RNA-SIP combined 13 with metabolic profiling of C-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. 1. Introduction overall population level. To obtain a more complete picture and a better understanding of functional features of the gut It is well documented that symbiotic gut inhabitants are microbiome in health and disease, we need to determine the required for maintaining host health and well-being [1, 2], as in situ metabolic function of individual species within this they greatly influence several host functions, not only those in complex microbial community. the intestinal system [3–8]. Despite the rapid development of Ingestion of prebiotic carbohydrates to boost health- next generation sequencing technologies, which provide deep promoting intestinal fermentation by selective enrichment insightintothestructureofthehumanmicrobiome[1],meta- and/or stimulation of the activity of commensal microorgan- bolically active populations in this complex community are isms that contribute to the well-being of their host is a viable still poorly described and incompletely understood. Hence, strategy to improve host health through the benefits of micro- there is still a large knowledge gap of the in situ functionality bial metabolism [9–11]. In particular short chain fatty acids of the gut microbiota and their metabolic capacities at an (SCFA), such as acetate, propionate, and butyrate produced 2 BioMed Research International during microbial fermentation, have attracted attention in as a starting point, future studies will address utilization of this regard. For instance, butyrate represents the main energy more complex carbohydrates, such as resistant starch (RS), source for colonocytes [12], and anti-inflammatory and by communities of mice origin in vivo to identify prebiotics immune-modulating effects of butyrate have been observed assimilating bacteria directly in the intestinal environment. [7, 13, 14]. However, knowledge about which microbial populations are stimulated by which carbohydrate under the 2. Material and Methods in situ conditions of the human gastrointestinal (GI) tract or other intestinal (model) systems is limited. The ability 2.1. Collection and Cultivation of Murine Faecal Samples. to link specific nutrient metabolizing processes to distinct C57BL/6J mice were raised at the animal facility at the groups of intestinal microorganisms would greatly expand University of Ulm under specific pathogen-free (SPF) con- the understanding of the dynamics of prebiotic carbohydrate ditions, receiving a standard laboratory diet and water ad utilization and their fate in the large bowel. libitum. Fresh faecal pellets were randomly collected from The stable isotope probing (SIP) technology [15] isa 12 healthy animals within 4 h of excretion. The pellets of all means of identifying microorganisms associated with various animals were finally pooled and subsequently homogenized assimilation and fermentation processes of highly isotope- in M9 minimal medium [34] supplemented with thiamin enriched compounds in environmental samples [16–19]. (2 mg/L) and Casamino Acids (1 g/L), lacking glucose at this RNA-SIP [20] offers the advantage of a rapid incorporation stage, to obtain a 15% (w/v) faecal slurry. Slurry material 13 of the stable isotope (e.g., C) into the RNA by metabolically (1 mL for each treatment) was mixed 1 : 1 with M9 minimal 13 ≥ active microorganisms because of a high RNA synthesis medium containing 80 mM of [U C]glucose ( 99 atom%) 13 rate [17]. This C-enriched RNA (“heavy” RNA) can then (Sigma-Aldrich GmbH, Steinheim, Germany), yielding a 12 final concentration of 40 mM glucose and 7.5% (w/v) of be separated from unlabeled C background RNA (“light” faecal material. Samples were incubated in individual 15 mL RNA) using isopycnic density gradient centrifugation [21, ∘ reaction tubes at 37 C for 0 h (control), 2 h, or 4 h under 22]. Further molecular characterization of the 16S rRNA in anaerobic conditions, which were obtained by using airtight the fractionated gradients links bacterial identity to metabolic jars and AnaeroGen sachets (Merck, Darmstadt, Germany) activity. This technology has been applied to a few gut resulting in a total of three different incubation treatments. microbiota before, studying the utilization of simple and Prior to use, the M9 minimal medium was filter sterilized, complex sugars [23–26], and it has been proven to provide ∘ deoxygenated, and prewarmed to 37 C. an effective link between the identity of microorganisms and the metabolic assimilation of a particular substrate in situ. Otherwise, this information can only be indirectly inferred 2.2. RNA Extraction, Isopycnic Centrifugation, Gradient Frac- from traditional enrichment type studies using nonlabeled tionation, and Quantification. After incubation, microbial cells from each incubation were harvested by centrifugation substrates. In addition, high pressure liquid chromatography ∘ × coupled to isotope ratio mass spectrometry (HPLC-IRMS) for 20 min at 4 C and 3220 g. Total RNA was extracted from 13 1 mL of each sample using the PowerMicrobiome RNA Isola- is a valuable technique for tracking the C-label down into tion Kit following the manufacturer’s instructions (MO Bio various metabolic products including volatile fatty acids [27– Laboratories Inc., Carlsbad, USA). Residual genomic DNA ∘ 29]. Their quantification and isotopic composition provide was removed by incubating the RNA (100 L) for 1 h at 37 C additional insight into the functioning of microbial com- with 10 L RNase-free DNase I (10 U/L; Roche, Mannheim, munities, as distinct populations can be linked to specific Germany), 15 Lof10xDNaseIbuffer(400mMTris-HCl, metabolic pathways [30, 31]. 100 mM NaCl, 60 mM MgCl2, 10 mM CaCl2, pH 7.9), and Animal models represent valuable and relatively easy 25 L of nuclease-free water. Further purification of the RNA accessible tools in gut microbiota research [32, 33]. In partic- samples was performed using Qiagen RNeasy spin columns ular in vivo studies are important for studying basic aspects of (Qiagen, Hilden, Germany) according to the manufacturer’s digestion, such as the microbial assimilation of prebiotic car- instructions. Subsequently, the RNA samples were quantified bohydrates, and help to unravel the functionality of the intes- using a P360 Nanophotometer (Implen GmbH, Munich, tinal microbiota and to better understand its role in health Germany) and the absence of genomic DNA was confirmed and disease. Here, to the best of our knowledge, RNA-SIP was by the absence of PCR products after amplification of 16S used for the first time in an intestinal environment of mice rRNA genes with universal primers 27F/907R [35, 36]. origin. In combination with metabolic profiling, bacteria Gradient ultracentrifugation