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Next generation sequencing based transcriptomic analysis of bile stress response in Bifidobacterium longum BBMN68

ABSTRACT: Bifidobacterium longum is one of the natural inhabitants in human gastrointestinal tract. In order to colonize and exert particular functions in the gut, it has to be tolerant to the physiological concentrations of bile salts. In this work, we used RNA-Seq transcriptomics based on the Next-Generation Sequencing to investigate the global response to bile in B. longum BBMN68, a potential probiotic strain isolated from a healthy centenarian. In the presence of 0.75 g liter-1 ox-bile, the transcription of 236 genes were regulated (≥ 3-fold, p < 0.001). Function analysis and Gene Ontology suggested that the bile stress response of B. longum BBMN68 covers almost all biological processes, including bile stress resistance, general stress response, central metabolic process, transmembrane transport, gene expression, cell proliferation and interaction with the host. Remarkably, 3 two-component systems and 11 transcription factors were up- or down-regulated by bile, and target genes of the regulators were identified by bacterial one-hybrid system and bioinformatics methods, resulting in a putative regulatory network that controls bile stress response in B. longum for the first time. This study significantly develops our understanding on bile stress response and brings new insight to the regulatory mechanism in bifidobateria.

ORGANISM(S): Bifidobacterium longum

PROVIDER: GSE46446 | GEO | 2014/06/29

SECONDARY ACCESSION(S): PRJNA200535

REPOSITORIES: GEO

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Next generation sequencing based transcriptomic analysis of bile stress response in Bifidobacterium longum BBMN68

Project description:Bifidobacterium longum is one of the natural inhabitants in human gastrointestinal tract. In order to colonize and exert particular functions in the gut, it has to be tolerant to the physiological concentrations of bile salts. In this work, we used RNA-Seq transcriptomics based on the Next-Generation Sequencing to investigate the global response to bile in B. longum BBMN68, a potential probiotic strain isolated from a healthy centenarian. In the presence of 0.75 g liter-1 ox-bile, the transcription of 236 genes were regulated (M-bM-^IM-% 3-fold, p < 0.001). Function analysis and Gene Ontology suggested that the bile stress response of B. longum BBMN68 covers almost all biological processes, including bile stress resistance, general stress response, central metabolic process, transmembrane transport, gene expression, cell proliferation and interaction with the host. Remarkably, 3 two-component systems and 11 transcription factors were up- or down-regulated by bile, and target genes of the regulators were identified by bacterial one-hybrid system and bioinformatics methods, resulting in a putative regulatory network that controls bile stress response in B. longum for the first time. This study significantly develops our understanding on bile stress response and brings new insight to the regulatory mechanism in bifidobateria. Whole mRNA profiles of B. longum BBMN68 growing in the absence (CK) and presence (OG) of ox-bile were generated using AB SOLiD technology and differentially expressed genes were anylyzed.

2014-06-29 | E-GEOD-46446 | biostudies-arrayexpress

Global transcriptional responses to a long-term treatment of bile salts in Bifidobacterium longum BBMN68

Project description:Purpose：Bifidobacteria are common inhabitants of the human gastrointestinal tract. In order to colonize in the gut, it is important to adapt to the physiological concentrations of bile salts. The global response to bile in B. longum BBMN68, isolated from a healthy centenarian in the Bama County of the Guangxi Zhuang Autonomous Region in China, has been investigated through RNA-seq transcriptomics sequencing in our previous work. However, a long-term bile salts treatment is more suitable to simulate the human gastrointestinal tract environment. The goals of this study are to invstigated the global response to a long-term treatment of bile salts in B. longum BBMN68. Methods: Samples from BBMN68 cultured with or without 0.75 g liter-1 ox-bile for 24 hours were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 11-13 million total mapped reads per sample.

2018-05-04 | GSE113993 | GEO

Next generation sequencing based transcriptomic analysis of bile stress response in Lactobacillus salivarius Ren

Project description:Lactobacillus salivarius is a member of the indigenous microbiota of the human gastrointestinal tract (GIT). Tolerance to bile stress is crucial for intestinal lactobacilli to survive in the GIT and to exert their beneficial actions. In this work, the Next-Generation Sequencing platform Illumina HiSeq 2000 was used to investigate the global response to bile in L. salivarius Ren, a potential probiotic strain isolated from a healthy centenarian. In the presence of 0.75 g liter-1 oxgall, the transcription of nearly 200 genes was detected to be associated with bile stress, including genes involved in carbohydrate and amino acid metabolism, cell envelope and fatty acid biogenesis, transcription and translation. This study improves our understanding on bile stress response in L. salivarius Ren.

2019-12-18 | GSE68033 | GEO

Bifidobacterium longum

Project description:Next generation sequencing based transcriptomic analysis of bile stress response in Bifidobacterium longum BBMN68

| PRJNA200535 | ENA

RNA sequencing of Bifidobacterium longum subsp. longum SC596 in response to various substrates

Project description:The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. longum SC596 to pooled and individual human milk oligosaccharides (HMO) relative to lactose

2016-10-08 | GSE87697 | GEO

Expression data from Bifidobacterium longum strains exposed to hydrogen peroxide stress

Project description:Stress survival tactics in bacteria utalize the up- and down-regulation of stress response genes. In bacterial that lack classical stress response genes for oxidative stress, other cellular systems can be used for cell survival. We used custom microarrays to study the regulation of genes in Bifidobacterium longum strains to oxidative stress to elucidate novel stress response mechanisms.

2013-02-28 | GSE44709 | GEO

Kolsto-B. cereus Transcriptional response of the B. cereus ATCC14579 wild type to bile salts stress

Project description:Comparison of the transcriptional response of B. cereus ATCC14579 before and after 15 min bile salts stress.

2012-01-31 | E-MEXP-3535 | biostudies-arrayexpress

RNA-Sequence analysis of enteroids incubating with Bifidobacterium longum

Project description:Although oral administration of Bifidobacterium longum (B. longum) relieves irritable bowel syndrome (IBS) symptoms in a clinical setting, the underlying mechanisms remain undetermined. Herein, we confirmed that B. longum ameliorated defecation habits and alleviated visceral hypersensitivity in water avoidance stress (WAS) rats. Further analysis revealed that B. longum enhanced mucosal repair, promoted the production of lysozyme, and ameliorated microbiota dysbiosis in WAS rats. These activities are all closely correlated with Paneth cell function. In vitro, we incubated primary cultured enteroids with B. longum and found that this bacterium promoted the proliferation of these organoids, which may be attributed to the up-regulated expression of the stem niche factors WNT3A and TGF-β which are serected by the Paneth cells. On the basis of our findings, we propose that B. longum relieves IBS by restoring the antimicrobial activity and stem niche maintenance functions of Paneth cells.

2020-05-01 | GSE149592 | GEO

Kolsto-Bacillus cereus transcriptional response of ATCC14579 BC4707 mutant to bile salts stress

Project description:Analysis of the transcriptional response of B. cereus ATCC14579 BC4707 deletion mutant after 15 min bile salts stress

2012-01-31 | E-MEXP-3536 | biostudies-arrayexpress

Next generation sequencing based transcriptomic analysis of oxidative stress response in Bifidobacterium longum BBMN68

Project description:Bifidobacterium longum strain BBMN68 is resistant to low concentrations of oxygen. In this study, a transcriptomic study was performed to detail the cellular response of B. longum strain BBMN68 to oxidative stress. Oxygen and its intermediate metabolites, reactive oxygen species (ROS), induced abundant changes in gene expression at the mRNA level. Increased expression was found for genes involved in ROS detoxification and the redox homeostasis system, protein and DNA synthesis and repair, the FeâS cluster assembly system, and biosynthesis of branched-chain amino acids and tetrahydrofolate. Among them, two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, were rapidly and persistently induced: first, the class Ib RNR NrdHIEF and then the class III RNR NrdDG. The increased resistance to oxygen and hydrogen peroxide conferred by NADH oxidase was confirmed by its heterogeneous overexpression in B. longum strain NCC2705. In addition, cell-membrane and cell-wall compositions were modified, probably by an increase in cyclopropane fatty acids and a decrease in polysaccharides, respectively, resulting in improved cell hydrophobicity and autoaggregation; this subsequently reduced the permeation of dissolved oxygen into the cell. Taken together, the proposed cell model of B. longum responses to oxygen stress suggests that this bacterium employs a complex molecular defense mechanism against oxygen-induced stresses. Whole mRNA profiles of B. longum BBMN68 grown in the absence or presence of 3% oxygen were generated using AB SOLiD technology and differentially expressed genes were analyzed.

2016-01-26 | E-GEOD-65320 | biostudies-arrayexpress

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