A platform for screening microbial effects on primary epithelial cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE231605 | GEO | 2023/05/15
REPOSITORIES: GEO
Similar Datasets
Project description:The deposited microarray data were generated in a study that integrated the gene expression profiles and metabolic responses of Caco2 cells incubated with Bifidobacterium infantis subsp. infantis and Salmonella enterica subsp. enterica sv. Typhimurium. The aim of this study was to investigate the interaction of B. infantis, S. Typhimurium, and host cells (Caco2) in the course of infection to understand the molecular mechanics of probiotic-pathogen-host interactions.
2024-05-08 | GSE266880 | GEO
Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.
2017-02-10 | GSE63950 | GEO
Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.
2017-02-10 | GSE64017 | GEO
Project description:Members of the serpin (serine protease inhibitor) superfamily have been identified in higher, multicellular eukaryotes, as well as in bacteria, although surveillance of available genome sequences indicates that bacterial serpin-encoding (ser) homologs are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least five, and perhaps up to nine, out of 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria specify serpins that form a separate clade. We characterized the ser210B locus of Bifidobacterium breve 210B, which consists of a number of genes, whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, micro array analysis, RT-PCR and Quantitative Real Time (qRT) - PCR analysis revealed that a 3.5 kb polycistronic mRNA, encompassing the ser210B operon with a single transcriptional start site, is strongly induced following treatment of B. breve 210B cultures with particular proteases. In contrast, transcription of the ser homolog of other bifidobacteria, such as Bifidobacterium longum subsp. infantis, Bifidobacterium dentium and B. longum subsp. longum, appears to be triggered by a different set of proteases Transcriptional response to protease treatments (kallikrein, papain and chymotrypsin) of Bifidobacterium breve 210B
2010-05-06 | E-GEOD-20626 | biostudies-arrayexpress
Project description:Recent studies have begun to elucidate the mechanisms of utilisation of some human milk oligosaccharides (HMO) components by Bifidobacterium breve. However, this phenomenon is still relatively poorly understood, with little to no work to date in understanding a number of specific structures common to HMO. In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of Lacto-N-Tetraose and Lacto-N-neoTetraose, which represent the central moieties of Type I and Type II HMOs, respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of these two HMO structures was identified and characterised. Homologs of tWe also identified the key genetic loci involved in the utilisation of these HMO substrates in B. breve, B. bifidum and B. longum subsp. infantis using bioinformatic analyses were shown to be, and noted the relatively variably present among other members ofscant distribution of their homologs across the Bifidobacterium genus as a whole, withwhile noting a distinct pattern of conservation of LNB utilisation genes inamong human-associated bifidobacterial species.
2017-02-09 | GSE84710 | GEO
Project description:Members of the serpin (serine protease inhibitor) superfamily have been identified in higher, multicellular eukaryotes, as well as in bacteria, although surveillance of available genome sequences indicates that bacterial serpin-encoding (ser) homologs are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least five, and perhaps up to nine, out of 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria specify serpins that form a separate clade. We characterized the ser210B locus of Bifidobacterium breve 210B, which consists of a number of genes, whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, micro array analysis, RT-PCR and Quantitative Real Time (qRT) - PCR analysis revealed that a 3.5 kb polycistronic mRNA, encompassing the ser210B operon with a single transcriptional start site, is strongly induced following treatment of B. breve 210B cultures with particular proteases. In contrast, transcription of the ser homolog of other bifidobacteria, such as Bifidobacterium longum subsp. infantis, Bifidobacterium dentium and B. longum subsp. longum, appears to be triggered by a different set of proteases
2010-03-09 | GSE20626 | GEO
Project description:Bifidobacterium longum subsp. infantis is a bacterial commensal that colonizes the breast-fed infant gut where it utilizes indigestible components delivered in human milk. Accordingly, human milk contains several non-protein nitrogenous molecules, including urea at high abundance. This project investigates the degree to which urea is utilized as a primary nitrogen source by Bifidobacterium longum subsp. infantis and incorporation of hydrolysis products into the expressed proteome.
2023-03-22 | PXD019401 | Pride
Project description:Dr. Lebrilla's lab is working on another set of transcriptomics experiments which will measure whether HMO (human milk oligosacharides) elicit a differential response on Caco2 in the presence of B.infantis. They wish to supplement the data obtained with the Illumina platform with glycan-related expression data obtained with the Gene-chips to achieve a more complete understanding on how Caco2 cells respond to the presence of HMOs and B.infantis. The transcriptomics data is being complemented by qPCR based bacterial-epithelial cells binding assays, and glycan arrays assays for which they have initiated a collaboration with the CFG Core H (David Smith). The influence, signaling and adhesion between Bifidobacterium infantis, a probiotic microorganism abundant in infant feces, and Caco2 epithelial cells. Our hypothesis is that HMOs act as signaling molecules for both Caco2 cells and B. infantis to indicate the presence in the gut, of a nutrient niche adapted for the nourishment and recruitment of HMO-consuming probiotic microorganism. HMOs therefore could play a role in the expression and binding to GBPs both on epithelial cells and in probiotic gut microorganisms. Preliminary transcriptomics data analysis obtained by using the Illumina Human Ref-8 Expression Bead Chip, has revealed that co-incubation of Caco2 cells with HMO upregulates genes belonging to chemokines, adhesion molecules, growth factors and glycan degradation, thus indicating that HMOs are actively recognized by these cells. We are working on another set of transcriptomics experiments which will measure whether HMO elicit a differential response on Caco2 in the presence of B.infantis. We wish to supplement the data obtained with the Illumina platform with glycan-related expression data obtained with the Gene-chips to achieve a more complete understanding on how Caco2 cells respond to the presence of HMOs and B.infantis. The transcriptomics data is being complemented by qPCR based bacterial-epithelial cells binding assays, and glycan arrays assays for which we have initiated a collaboration with the CFG Core H (David Smith). We are requesting the analysis of 16 RNA samples from Caco2 cells on the Glyco-gene chips, for testing respectively 4 independent biological replicates for each of the 4 different co-incubation conditions. RNA preparations from Caco2 cells were sent to Microarray Core (E). The RNA was amplified, labeled, and hybridized to GLYCO_v3 microarrays.
2011-06-14 | E-GEOD-29934 | biostudies-arrayexpress
Project description:Bifidobacterium longum subsp. infantis (B. infantis) is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. infantis; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of genomic loci encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR effectors. Reconstruction of NagR regulons in various Bifidobacterium lineages revealed multiple regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling foraging of mixtures of GlcNAc-containing host-derived glycans in mammalian gut-colonizing B. infantis and Bifidobacterium bifidum.
2022-04-02 | GSE196064 | GEO
Project description:we investigated the effect of linoleic acid on the metabolism Bifidobacterium breve DSM 20213 by means of transcriptomic approach
2019-10-24 | GSE139284 | GEO