Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

Abstract

Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1 À / À and wild-type mice, as determined by 454 pyrosequencing of bacterial 16S rRNA (gene) amplicons, metatranscriptomics and quantitative fluorescence in situ hybridization of selected phylotypes. The bacterial families Ruminococcaceae, Bacteroidaceae, Enterobacteriaceae, Deferribacteraceae and Verrucomicrobiaceae increased in relative abundance in DSS-treated mice. Comparative 16S rRNA sequence analysis at maximum possible phylogenetic resolution identified several indicator phylotypes for DSS treatment, including the putative mucin degraders Akkermansia and Mucispirillum. The analysis additionally revealed strongly contrasting abundance changes among phylotypes of the same family, particularly within the Lachnospiraceae. These extensive phylotype-level dynamics were hidden when reads were grouped at higher taxonomic levels. Metatranscriptomic analysis provided insights into functional shifts in the murine intestinal microbiota, with increased transcription of genes associated with regulation and cell signaling, carbohydrate metabolism and respiration and decreased transcription of flagellin genes during inflammation. These findings (i) establish the first in-depth inventory of the mouse gut microbiota and its metatranscriptome in the DSS colitis model, (ii) reveal that family-level microbial community analyses are insufficient to reveal important colitisassociated microbiota shifts and (iii) support a scenario of shifting intra-family structure and function in the phylotype-rich and phylogenetically diverse Lachnospiraceae in DSS-treated mice.

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

“…2C, SI Results and Discussion), we analyzed nonembedded lumen contents. We applied a suite of probes based on abundant bacterial groups in a previous study of dextran sodium sulfate (DSS)-induced acute colitis in the same mice (8). These probes were specific for Akkermansia spp., Bacteroides acidifaciens, Mucispirillum spp., Lactobacillaceae/Enterococcaceae spp., and a Ruminococcaceae OTU_5807 species-level phylotype.…”

“…Results produced from simplified model systems and metaomics studies are valuable for generating hypotheses, but techniques to directly probe important intestinal processes such as host-compound foraging are urgently needed to test these hypotheses (8). Here, we explored host-compound foraging using a stable isotope tracer-based approach for in vivo labeling and quantitative imaging of individual gut bacteria with high-resolution secondary ion mass spectrometry (NanoSIMS).…”

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

“…The divergent response of members of the Ruminococcaceae with respect to BMI z ‐score may indicate different niche preferences within this group and may also help to explain why the increased Firmicutes / Bacteroidetes ratio is not found in all studies, as it groups together Firmicutes populations with discordant shifts in obesity. Divergent responses of members of the clostridia have previously been observed in other conditions such as inflammation (Berry et al ., 2012). It is likely that the extensive physiological and metabolic diversity in members of the clostridia is responsible for these contrasting responses, and additional studies are needed to better characterize and functionally categorize the members of this abundant group.…”

High-fat diet alters gut microbiota physiology in mice

“…The probes used in the present study were Bac-0303 5 0 -CCA ATG TGG GGG ACC TT-3 0 (Manz et al, 1996) and Erec-0482 5 0 -CGC GGC ATT GCT CGT TCA-3 0 (Franks et al, 1998) (Thermo Fisher Scientific, Vienna, Austria). Cecal samples that had been fixed in 4% paraformaldehyde were hybridized on aluminum slides using a previously described hybridization protocol (Berry et al, 2012). Spectra of cells from target populations were acquired using a LabRAM HR800 confocal Raman microscope (Horiba Jobin-Yvon, Munich, Germany) equipped with a 532 nm Nd:YAG laser as described previously (Haider et al, 2010).…”