Project description:We compared the microbiota of paired mouse caecal contents and faeces by applying a multi-omic approach, including 16S rDNA sequencing, shotgun metagenomics, and shotgun metaproteomics. The aim of the study was to verify whether faecal samples are a reliable proxy for the mouse colonic luminal microbiota, as well as to identify changes in taxonomy and functional activity between caecal and faecal microbial communities, which have to be carefully considered when using stool as sample for mouse gut microbiota investigations.
2017-03-31 | PXD004911 | Pride
Project description:EMG produced TPA metagenomics assembly of the Comparison between mouse caecal contents and faeces (Mouse_caecal_contents_vs_faeces) data set.
Project description:Caecal contents from three specific pathogen-free (SPF) mice, and three germ-free (GF) mice were analyzed by DIA-MS (SWATH-MS) using TripleTOF 5600+ (SCIEX). Paraprevotella clara (P. clara) culture supernatants nontreated and treated tunicamycin or 2-fluro-L-fucose (2F-Fuc) were analyzed by DIA-MS using Q Exactive HF-X (Thermo Fisher Scientific). In addition, GF mouse caecal contents were incubated with P. clara or medium control. Supernatant samples were collected at the indicated time points and subjected to peptidome analysis using Q Exactive HF-X (Thermo Fisher Scientific).
Project description:Campylobacter jejuni is the major cause of acute gastroenteritis in the developed world. It is usually acquired through contaminated poultry as C. jejuni causes a silent asymptomatic infection of the chicken. Pathogens face different sources of stress during its transit through the gut. In this study, we describe the ability of C. jejuni to survive nitrosative stress at very low oxygen levels that reflect those in hypoxic gut environments. Specifically, we here explore an innovative model of signal recognition during colonization. We use a diffusion capsule to feed small, diffusible molecules from chicken caecal matter into a microaerobic C. jejuni culture to study the transcriptomic changes mounted as response to chemical signals present in the chicken gut. We find that in early stages of exposure to the caecal contents (10 min) the dual component colonization regulator, dccR, plays an important yet not fully understood role. Although the caecal material contains cyanide derived from plant sources, we find no role for a truncated globin (encoded by ctb), which has previously been implicated in resistance to this haem ligand.
Project description:RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference. Keywords: Disease state analysis, infected versus uninfected, common reference Five replicates from infected chick caecal contents compared to a common reference. Three replicates from in vitro grown Salmonella compared to a common reference. The common reference was genomic DNA and always occupies the Cy3 channel (channel 2).