Rat gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA421636 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6387630_1.fastq.gz | Fastqsanger.gz | |||
| SRR6387630_2.fastq.gz | Fastqsanger.gz | |||
| SRR6387640_1.fastq.gz | Fastqsanger.gz | |||
| SRR6387640_2.fastq.gz | Fastqsanger.gz | |||
| SRR6387650_1.fastq.gz | Fastqsanger.gz |
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Project description:Gradual changes of gut microbiota and metabolism in weaned rats with Lactobacillus acidophilus NCFM and Bifidobacterium lactis Bi-07 supplementation
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Project description:Analysis of differentiated Caco-2 intestinal epithelial cell line cocultured with probiotics L. acidophilus NCFM™, B. lactis 420, L. salivarius Ls-33 bacterial cells or treated with cell-free supernatant, and with E. coli O157:H7 cell-free supernatant. Lactobacillus and Bifidobacterium are important genera suggested to be beneficial for human health and E. coli O157:H7 is a pathogen causing hemorrhagic colitis and hemolytic uremic syndrome. Results provide insight into the mechanisms underlying the beneficial effects of probiotics on intestinal epithelial cells and a comparison to pathogenic E. coli.
2009-04-11 | GSE15636 | GEO
Project description:Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-β, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-β. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism. In the experiment saline control, Lactobacillus acidophilus NCFM, Bifidobacterium bifidum Z9 or both bacteria were were added to murine dendritic cells and stimulated for 10 hours. Experiments were run in triplicates and analyzed in a Two-way ANOVA design.
2010-02-24 | E-GEOD-20302 | biostudies-arrayexpress
Project description:Bifidobacterium animalis subsp. lactis Bi-07 Genome sequencing
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Project description:Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-β, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-β. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism.
2010-02-13 | GSE20302 | GEO
Project description:Helicobacter pylori causes chronic gastritis and avoids elimination by the immune system of the infected host. The commensal bacterium Lactobacillus acidophilus has been reported to exert beneficial effects as a supplement during H. pylori eradication therapy. In the present study, we applied whole genome microarray analysis to compare the immune response induced in murine bone marrow derived macrophages (BMDM) stimulated with L. acidophilus, H. pylori, or with both bacteria in combination Microarray expression profiling was performed to analyze stimulation of bone marrow derived macrophages with Helicobacter pylori 251, Lactobacillus acidophilus NCFM or Lactobacillus acidophilus NCFM co-stimulated with Helicobacter pylori 251 were analyzed 5 hours after infection.
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Project description:Interventions: This is a three-arm, single-blind, randomized controlled clinical trial. Patients (n = 36) will be randomly distributed into three blocks (G1,G2,G3). Patients will be randomly assigned to three blocks (G1,G2,G3) in a 1:1 ratio to receive probiotics (G1 group) with formulation: Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37 TM, Bifidobacterium lactis Bi-04TM, Bifidobacterium lactis Bi-07TM, Bifidobacterium bifidum Bb-02TM), associated with a standard nutritional guidance protocol. In the G2 (control) group, conventional treatment will be performed with a standard nutritional guidance protocol, without the use of probiotics. The intervention product (probiotic capsules) will be distributed and packaged according to the days of the research and inpatient ward, which will not be disclosed during the entire period of the research, the tests will be carried out on alternate days as detailed in the recruitment, in order not to cross-referencing of information between previously blinded participants. In the case of the G3 group, they will receive the probiotic capsules at the same time as the G1 group. Both groups that will use probiotic capsules should continue using them for 7 days, without any break in follow-up. The groups will be monitored twice a day in person or by telephone, in order to avoid loss of capsule intake.;G07.203.300.456.500
Primary outcome(s): To evaluate the use of perioperative probiotics to improve the nutritional and immunological clinical status of patients undergoing gastrectomy for gastric cancer
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Project description:Lactobacilli are probiotics that, among other health promoting effects, have been ascribed immunostimulating and virus preventive properties. Certain lactobacilli species have been shown to possess strong IL-12 inducing properties. As IL-12 production depends on the up-regulation of type I interferons, we hypothesized that the strong IL-12 inducing capacity of L. acidophilus NCFM in murine bone marrow derived DC is caused by an up-regulation of IFN-β, which subsequently stimulates the induction of IL-12 and the dsRNA binding toll like receptor (TLR)-3. The expression of the genes encoding IFN-β, IL-12, IL-10 and TLR-3 in DC upon stimulation with L. acidophilus NCFM was measured. L. acidophilus NCFM induced a much stronger expression of ifn-β, il-12 and il-10 compared to the synthetic dsRNA ligand Poly I:C, whereas the levels of expressed tlr-3 were similar. By the use of whole genome microarray gene expression, we investigated whether other genes related to the viral defence were up-regulated in DC upon stimulation with L. acidophilus NCFM and found that various virus defence related genes, both early and late, were among the strongest up-regulated genes. The IFN-β stimulating capability was also detected in another L. acidophilus strain, but was not a property of other probiotic bacteria tested (B. bifidum and E. coli nissle).The IFN-β inducing capacity was markedly reduced in TLR-2 -/- DCs, dependent on endocytosis and the major cause of the induction of il-12 and tlr-3 in L. acidophilus NCFM stimulated cells. Collectively, our results reveal that certain lactobacilli trigger the expression of viral defence genes in DC in a TLR-2 manner through induction of IFN- β.
2009-10-08 | GSE18460 | GEO
Project description:This study reports an over 20-fold increase in the adhesive ability of Lactobacillus acidophilus NCFM to Caco-2 cells following a 1 hour incubation of cells that were concentrated ten-fold, immediately prior to adhesion. Microarray analysis of the global transcriptional response with and without exposure to the adhesion adaptive conditions revealed several genes potentially involved with adhesion to the intestinal epithelial cells and a classic stress response. Interestingly, putative genes linked to the synthesis of an interspecies signaling molecule, autoinducer-2 (AI-2), were overexpressed. Examination of the L. acidophilus NCFM genome revealed the complete pathway for AI-2 synthesis. AI-2 activity was detected in L. acidophilus NCFM during stationary growth phase using the Vibrio harveyi BB170 assay system. Using site-specific integration, an isogenic mutation was created in luxS and the resulting derivative of L. acidophilus NCFM did not produce AI-2. A 58 % decrease in adherence to Caco-2 cells was also observed by the LuxS- mutant when the cells were used for adhesion directly from logarithmic phase cultures. However, the LuxS- mutant strain still responded to adhesion adaptive conditions with significantly increased adherence indicating that additional factors contribute to the amplified adhesion response. Keywords: Culture response to specific environmental conditions
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Project description:Lactobacilli are probiotics that, among other health promoting effects, have been ascribed immunostimulating and virus preventive properties. Certain lactobacilli species have been shown to possess strong IL-12 inducing properties. As IL-12 production depends on the up-regulation of type I interferons, we hypothesized that the strong IL-12 inducing capacity of L. acidophilus NCFM in murine bone marrow derived DC is caused by an up-regulation of IFN-β, which subsequently stimulates the induction of IL-12 and the dsRNA binding toll like receptor (TLR)-3. The expression of the genes encoding IFN-β, IL-12, IL-10 and TLR-3 in DC upon stimulation with L. acidophilus NCFM was measured. L. acidophilus NCFM induced a much stronger expression of ifn-β, il-12 and il-10 compared to the synthetic dsRNA ligand Poly I:C, whereas the levels of expressed tlr-3 were similar. By the use of whole genome microarray gene expression, we investigated whether other genes related to the viral defence were up-regulated in DC upon stimulation with L. acidophilus NCFM and found that various virus defence related genes, both early and late, were among the strongest up-regulated genes. The IFN-β stimulating capability was also detected in another L. acidophilus strain, but was not a property of other probiotic bacteria tested (B. bifidum and E. coli nissle).The IFN-β inducing capacity was markedly reduced in TLR-2 -/- DCs, dependent on endocytosis and the major cause of the induction of il-12 and tlr-3 in L. acidophilus NCFM stimulated cells. Collectively, our results reveal that certain lactobacilli trigger the expression of viral defence genes in DC in a TLR-2 manner through induction of IFN- β. Experiment Overall Design: In the experiment Lactobacillus NCFM were added to murine dendritic cells and stimulated for 4, 10 or 18 hours. These were compared to control experiment at the same timepoints. Experiments were run in triplicates except for control 10h and control 18h which were only in duplicate, giving a total of 16 arrays.
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