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RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

ABSTRACT: RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

PROVIDER: PRJNA505334 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8182820_1.fastq.gz	Fastqsanger.gz
	SRR8182820_2.fastq.gz	Fastqsanger.gz
	SRR8182821_1.fastq.gz	Fastqsanger.gz
	SRR8182821_2.fastq.gz	Fastqsanger.gz
	SRR8182822_1.fastq.gz	Fastqsanger.gz

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RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

Project description:Purpose: To understand the metabolic mechanism of Lactobacillus salivarius Ren in raffinose Methods: Samples of Lactobacillus salivarius Ren grown in glucose and raffinose were sequenced on the Illumina Hiseq platform. Three independent biological replicates were generated, including a total of six samples. 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 8-10 million total mapped reads per sample.

2018-11-14 | GSE122483 | GEO

Global transcriptomic analysis of the Raffinose Utilization in Lactobacillus salivarius Ren

Project description:This study was aimed to further illustrate the expression files of REN between glucose and raffinose in MRS broth. Transcriptomic analysis combined with mutants of the key genes based on homologous recombination technology indicated that galA1 gene cluster plays an important role in raffinose metabolism. Gene rafP and galA1 are responsible for raffinose transport and α-galactoside hydrolysis, followed by galactose hydrolysis by galKTE and sucrose hydrolysis by scrB. Lactobacillus salivarius Ren expanded the carbon utilization spectrum to adapt the fluctuating carbohydrate sources in the environment and shifted its carbohydrate metabolism to mixed-acid fermentation and then generated extra energy to bacterial growth when exposed to raffinose.

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Global transcriptomic analysis of the Raffinose Utilization in Lactobacillus salivarius Ren

Project description:Global transcriptomic analysis of the Raffinose Utilization in Lactobacillus salivarius Ren

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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.

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Ligilactobacillus salivarius str. Ren

Project description:Ligilactobacillus salivarius str. Ren Genome sequencing

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Transcription profiling of Lactobacillus salivarius bile response_LS201

Project description:Porcine bile induced transcriptome of Lactobacillus salivarius

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

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Transcription profiling of Lactobacillus salivarius bile response_LS201bsh knockout

Project description:bile induced transcriptome of Lactobacillus salivarius LS201bsh ko.

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A long and abundant non-coding RNA (lancRNA) in Lactobacillus salivarius

Project description:Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbor at least one megaplasmid which encodes functions contributing to contingency metabolism and environmental adaptation. RNA-seq transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel long and unusually abundant non-coding RNA (lancRNA) encoded by the megaplasmid and which represented more than 75% of total RNA-seq reads after depletion of ribosomal RNA species. The expression level of this 550 nt lancRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time, and was also expressed during intestinal transit in a mouse. This lancRNA sequence is specific to the L. salivarius species, however among 45 L. salivarius genomes analyzed, not all (only 34) harbored the sequence for the lancRNA. This lancRNA was produced in 27 tested L. salivarius strains but at strain-specific expression levels. High-level lancRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lancRNA identified altered expression levels of genes in a number of pathways but a definitive function of this new long non-coding RNA was not identified. This lancRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.

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Comparison of gene transcription in Caco-2 cells stimulated with Lactobacillus salivarius UCC118 with that in unstimulated cells.

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