Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM
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ABSTRACT:
ORGANISM(S): Lactobacillus acidophilus NCFM
PROVIDER: GSE35968 | GEO | 2012/12/20
SECONDARY ACCESSION(S): PRJNA151615
REPOSITORIES: GEO
Similar Datasets
Project description:The global transcriptome of the wild type Lactobacillus acidophilus NCFM strain (NCK56) was measured during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate. Oligoarray hybridization experiments were performed to compare the differential transcriptional profiles of the NCK56 at the early-log (OD600nm 0.3-0.5) phase when cultured in semi-synthetic medium (SSM, Barrangou et al., 2003 PNAS. 100:8957-8962, supplemented with a range of 1% (w/v) carbohydrates, at 37 M-BM-0C and harvested by centrifugation and flash freezing. A total of 12 NCK56 cultures were prepared by growing in SSM supplemented with each one of the 12 tested carbohydrates. Each culture was grown in fresh carbohydrate supplemented SSM with a 1% inoculum from an overnight culture for a total of five subcultured passages. Aliquots of cells were collected at OD600nm of 0.3-0.5 (early log-phase) for total RNA extraction and cDNA synthesis. Labeled cDNA samples from NCK56 were coupled with mono-reactive Cy3 and Cy5 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), for two technical replicates on each carbohydrate (e.g. cy3-GOS and cy5-GOS). Comparative hybridizations were performed on samples representing two different carbohydrate cultures at same growth phases labeled with either cy3 or cy5 using a loop design for 12 hybridizations.
2012-12-20 | E-GEOD-35968 | biostudies-arrayexpress
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.
2013-07-02 | E-GEOD-42622 | biostudies-arrayexpress
Project description:We used a whole genome array containing 97.4 % of the annotated genes of Lactobacillus acidophilus NCFM, a probiotic culture that belongs to the lactic acid bacteria group, to identify genes that are differentially expressed under several stress conditions. Keywords: Stress response
2005-12-08 | GSE2782 | GEO
Project description:Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM
| PRJNA151615 | ENA
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
2010-02-09 | GSE5674 | GEO
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.
2009-10-20 | E-GEOD-18460 | biostudies-arrayexpress
Project description:A L. acidophilus NCFM mutant (NCK1909) carrying an in-frame deletion within the upp gene (LBA0770) was constructed as a background host for a newly developed upp-based counterselectable gene replacement system for L. acidophilus. Since the NCK1909 mutant serves both as the host for genetic exchange and the reference strain for subsequent phenotypic studies of deletion mutants that will be generated from the counterselective gene replacement system, comparative gene expression study was performed to ensure the genotype of NCK1909 is representative of the NCFM parent strain.
2009-03-24 | GSE14622 | GEO
Project description: Not available
| S-EPMC3446993 | biostudies-literature
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: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