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In vitro and in vivo transcriptomics profile of Lactobacillus johnsonii MR1

ABSTRACT: in vitro and in vivo transcriptomics profile of Lactobacillus johnsonii MR1

PROVIDER: PRJNA1133651 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29751508_1.fastq.gz	Fastqsanger.gz
	SRR29751508_2.fastq.gz	Fastqsanger.gz
	SRR29751509_1.fastq.gz	Fastqsanger.gz
	SRR29751509_2.fastq.gz	Fastqsanger.gz
	SRR29751510_1.fastq.gz	Fastqsanger.gz

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Project description:Work with pathogens like Vibrio cholerae has shown major differences between gene expression in bacteria grown in vitro and in vivo. To explore this subject for commensals, we investigated the transcription of the Lactobacillus johnsonii NCC533 genome during in vitro using the microarray technology. In broth growth, 537, 626 and 277 of the 1756 tested genes were expressed during exponential, “adaptation” (early stationary phase) and stationary phase, respectively. One hundred-one, 150 and 33 genes, respectively, were specifically transcribed in these three phases. Forty-four per cent of the NCC533 genome were not detectably transcribed under any of the investigated conditions. Non-transcribed genes were clustered on the genome and enriched in the variable genome part. For gene expression profiling experiments, cells were grown in a Sixfors fermentor system, composed of four individual 500 ml vessels (Infors, Bottmingen, Switzerland). Growth curves were performed at least in triplicate using the four separate fermentation vessels (fermentor 1 to 4), which were inoculated at 0.4% (v/v) with four individual overnight cultures in order to reach a starting optical density (OD600nm) of 0.05. Samples were taken at regular intervals from the four vessels to measure the OD600 nm and determine the CFU/ml until 36 h of fermentation. Aliquots of 15 ml (for early (T1-T2) and mid-exponential phases (T3-T4)) and 10 ml (for adaptation (T5), mid-stationary (T6) and late stationary phases (T7)) were centrifuged for 5 min at 10,000 x g at 4°C. Cell pellets were snap frozen in liquid nitrogen and stored at –80°C until further use.L. johnsonii NCC533 was grown in MRS broth supplemented with 2 % glucose as carbon source and 0.05% cysteine as redox buffer. For mRNA isolation L. johnsonii NCC533 cells were harvested from the broth culture several time points after inoculation (Fig. 1). In a total of 27 hybridization experiments. Genes were scored as expressed when their signal was detected in all hybridization experiments (with two technical replicates per slide) with mRNA preparations obtained from three independent growth experiments. Keywords: Growth phases of Lactobacillus johnsonii NCC533 in MRS

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In vitro and in vivo transcriptomics profile of Lactobacillus johnsonii MR1

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