Project description:This study generated spatial transcriptomic profiles of ileum, cecum, and colon from specific pathogen-free (SPF) and germ-free (GF) Kunming (KM) mice using the BGI Stereo-seq platform. The dataset captures spatial organization and segment-specific immune niches in the absence of microbiota.
Project description:This dataset serves as a validation cohort for single-cell transcriptomic changes observed in germ-free (GF) and specific pathogen-free (SPF) mice. Single-cell RNA sequencing was performed on B cell, T cell, and myeloid subsets isolated from the colon of C57BL/6 mice. The dataset captures immune heterogeneity in the absence of microbiota and enables direct comparison with the KM mouse cohort.
Project description:Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum, and proximal colon under three colonization states: germ-free, monocolonized with Bacteroides thetaiotaomicron, and conventionally raised. Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal tract. Unsupervised clustering showed that host protein abundance primarily depended on gastrointestinal location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between conventionally raised mice relative to germ-free and monocolonized mice. Finally, comparison to fecal proteomic datasets suggested that the identities of stool proteins are not biased to any region of the gastrointestinal tract, but are substantially impacted by the microbiota in the distal colon.
Project description:This study generated a single-cell transcriptomic atlas of multiple intestinal segments (jejunum, ileum, cecum, and colon) from specific pathogen-free (SPF) and germ-free (GF) Kunming (KM) mice. The dataset captures immune heterogeneity and segment-specific transcriptional programs in the absence of microbiota.
Project description:To understand the effect of microbes on microRNAs in aorta, in this study, we examined expression of microRNA in the aorta of male (10 weeks old) germ-free mice and pathogen-free mice (control).
Project description:Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of diseases or disorders in an enteric-flora dependent manner. Here, we performed transcriptome analysis using Affymetrix GeneChip on large intestine (LI) of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR, and BALB/c SPF mice. Male germ-free (GF) and specific pathogen-free (SPF) mice of IQI and BALB/c strains were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C. Nine week old mice (n=3) were sacrificed by cervical dislocation and the intestines were dissected. comparison of the mice with or without enteric flora; comparison of the mice of different strains
