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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Germ-free and anti-biotic treated rats

ABSTRACT: The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats. Germ-free vs. non-germ-free, antibiotic treated vs. untreated

ORGANISM(S): Rattus norvegicus

SUBMITTER: James Sidaway

PROVIDER: E-GEOD-21937 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Germ-free and anti-biotic treated rats

Project description:The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats.

2010-08-31 | GSE21937 | GEO

Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on small intestines on germfree mice

Project description:Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of disease or disorders in an enteric-flora dependent manner. Here, we performed transcriptome analysis using Affymetrix GeneChip on small intestine (SI) of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR. Male germ-free (GF) and specific pathogen-free (SPF) IQI mice 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

2011-09-13 | E-GEOD-32084 | biostudies-arrayexpress

Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on large intestines on germfree mice

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

2011-09-13 | E-GEOD-32083 | biostudies-arrayexpress

Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression

Project description:Inappropriate cross talk between mammals and their gut microbiota may trigger intestinal inflammation and drive extra-intestinal immune-mediated diseases. Studies with germ-free or gnotobiotic animals represent the gold standard for research on bacterial-host interaction but they are not readily accessible to the wide scientific community. We aimed at refining a protocol that in a robust manner would deplete murine intestinal microbiota and prove to have significant biologic validity. Previously published protocols for depleting mice of their intestinal microbiota by administering broad-spectrum antibiotics in drinking water were difficult to reproduce. We show that twice daily delivery of antibiotics by gavage depleted mice of their cultivable fecal microbiota and reduced the fecal bacterial DNA load by approximately 400 fold while ensuring the animals’ health. Mice subjected to the protocol for 17 days displayed enlarged ceca, reduced Peyer’s patches and small spleens. Antibiotic treatment significantly reduced the expression of antimicrobial factors and altered the expression of 517 genes in total in the colonic epithelium. Genes involved in cell cycle were significantly altered concomitant with reduced epithelial proliferative activity in situ assessed by Ki-67 expression, suggesting that commensal microbiota drives cellular proliferation in colonic epithelium. We present a robust protocol for depleting mice of their cultivatable intestinal microbiota with antibiotics by gavage and show that the biological effect of this depletion is phenotypic characteristics and epithelial gene expression profile similar to those of germ-free mice. Comparison of genome-wide gene expression of colon intestinal epithelial cells from mice subjected to microbiota depletion protocol against to control mice.

2011-08-14 | E-GEOD-22648 | biostudies-arrayexpress

Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on small intestines on germfree mice

2011-09-14 | GSE32084 | GEO

Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on large intestines on germfree mice

2011-09-14 | GSE32083 | GEO

Short Chain Fatty Acid Independent Hepatic Histone Acetylation Patterns, Induced by Microbiota Exposure, are Irreversible

Project description:Germ-free mice are an indispensable tool in studying the gut microbiome and its effects on host physiology, though they are phenotypically different than their conventional counterparts. While antibiotic mediated microbiota depletion in conventional mice mimics the germ-free state, the scope of these reversible changes is unknown. We demonstrate robust hepatic transcriptomic alterations after antibiotic-mediated microbiota depletion together with depletion of luminal and portal vein levels of SCFAs though hepatic histone acetylation states remained largely unchanged.

2023-01-25 | GSE144266 | GEO

Variability of gene expression profiles in neutrophils from Germ-free mice

Project description:Neutrophils, key cells of the innate immune system, are responsible for preventing bacterial infections. It was already demonstrated that albeit neutrophils synthesize lower levels of protein and RNA they are able to marked change its gene expression after bacteria exposure. The absence of microbial stimulation has consequences on development of the mucosal immune system as demonstrated using germ-free mice as a model. We are interested in understanding if commensal flora induces changes in the gene expression profile of neutrophils in its site of production, the bone marrow. Total RNA obtained from isolated neutrophils from Bone Marrow from Germ-free mice and control

2013-03-30 | E-GEOD-43511 | biostudies-arrayexpress

Mice with and without enteric flora

Project description:Although microbiota plays a critical role for the normal development and function of host immune systems, the detail of the influence, especially on those in the large intestine (LI), remains unknown. Here, we performed transcriptome analysis using Affymetrix GeneChip on LI of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR. Keywords: comparison of the mice with or without enteric flora

2007-06-06 | GSE8006 | GEO

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences [RNA-Seq]

Project description:Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP), delivered from birth, induces metabolic alterations and affects ileal expression of genes involved in immunity. LDP that is limited to early life transiently perturbs the microbiota, which is sufficient to induce sustained effects on body composition, indicating that microbiota interactions in infancy may be critical determinants of long-term host metabolic effects. In addition, LDP enhances the effect of high-fat diet induced obesity. The growth promotion phenotype is transferrable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics per se, play a causal role. These studies characterize important variables in early-life microbe-host metabolic interaction and identify several taxa consistently linked with metabolic alterations. Male and female mice were exposed to low-dose penicillin from birth. In a second experiment, microbiota from female control and LDP mice was transferred to 3-week old female germ-free mice. Livers were collected at 8 weeks of age, RNA was extracted, and transcriptional differences were measured by RNAseq.

2014-09-01 | E-GEOD-58089 | biostudies-arrayexpress

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