Lactobacillus Firm5 in vivo and in vitro RNA sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactobacillus melliventris Lactobacillus helsingborgensis Lactobacillus apis Lactobacillus kullabergensis
PROVIDER: GSE166724 | GEO | 2021/02/13
REPOSITORIES: GEO
Similar Datasets
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
2008-01-17 | GSE9236 | GEO
Project description:Lactobacillus johnsonii, a Gram-positive, gut bacterium is well studied for its several health-beneficial properties. This
2024-07-15 | GSE271801 | GEO
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with oleuropein. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile shows that Lactobacillus plantarum WCFS1 adapts its metabolic capacity to acquire certain carbohydrates and repress the expression of genes involved in fatty acid biosyntheis. The transcriptomic datasets also revealed the downregulation of genes related to the biosynthesis of capsular polysaccharides and genes coding for ABC-type transporters. In addition, induction of oligopeptide permeases is also part of the response of Lactobacillus plantarum WCFS1 to oleuropein.
2019-10-21 | GSE90719 | GEO
Project description:Lactobacillus reuteri 100-23 is an autochthonous inhabitant of the rodent gastrointestinal system that adheres to the non-secretory epithelium of the forestomach and forms biofilms. Microarray analysis of the expression profile of L. reuteri 100-23 cells harvested from the stomach of ex-Lactobacillus-free mice, compared to those of L. reuteri 100-23 in laboratory culture, revealed an in vivo upregulation of a urease gene cluster by greater than 50-fold. Genes for urease production were absent in all publically available Lactobacillus genome sequences except L. reuteri 100-23 and have recently been identified as specific to rodent strains of L. reuteri (Frese et al. 2011). In the current study, the urease enzyme was shown to be functional. Supplementation with 2% urea allowed L. reuteri 100-23 to increase the pH of the culture medium. A mutant strain of L. reuteri 100-23 was developed by insertional inactivation of the ureC gene, which encodes the largest subunit of the urease enzyme. The mutant strain was unable to hydrolyze urea to increase the pH of culture medium, and did not survive acid stress at pH 2.5 for 6 h, even in the presence of urea. In contrast, the wild type strain was still viable after 6 h when 2% urea supplementation was included. When mice free of lactobacilli were inoculated with a mixture of equal numbers of wild type L. reuteri 100-23 and ureC mutant cells, the wild type constituted 99% of the resulting Lactobacillus population in the stomach, caecum and jejunum after one week (108 cells/gram of sample). This study has therefore shown the importance of a functional urease enzyme in the ecological fitness of L. reuteri 100-23. Analysis of the microarray data was obtained from two independent biological replicates.
2012-09-30 | E-GEOD-36286 | biostudies-arrayexpress
Project description:Lactobacillus reuteri 100-23 is an autochthonous inhabitant of the rodent gastrointestinal system that adheres to the non-secretory epithelium of the forestomach and forms biofilms. Microarray analysis of the expression profile of L. reuteri 100-23 cells harvested from the stomach of ex-Lactobacillus-free mice, compared to those of L. reuteri 100-23 in laboratory culture, revealed an in vivo upregulation of a urease gene cluster by greater than 50-fold. Genes for urease production were absent in all publically available Lactobacillus genome sequences except L. reuteri 100-23 and have recently been identified as specific to rodent strains of L. reuteri (Frese et al. 2011). In the current study, the urease enzyme was shown to be functional. Supplementation with 2% urea allowed L. reuteri 100-23 to increase the pH of the culture medium. A mutant strain of L. reuteri 100-23 was developed by insertional inactivation of the ureC gene, which encodes the largest subunit of the urease enzyme. The mutant strain was unable to hydrolyze urea to increase the pH of culture medium, and did not survive acid stress at pH 2.5 for 6 h, even in the presence of urea. In contrast, the wild type strain was still viable after 6 h when 2% urea supplementation was included. When mice free of lactobacilli were inoculated with a mixture of equal numbers of wild type L. reuteri 100-23 and ureC mutant cells, the wild type constituted 99% of the resulting Lactobacillus population in the stomach, caecum and jejunum after one week (108 cells/gram of sample). This study has therefore shown the importance of a functional urease enzyme in the ecological fitness of L. reuteri 100-23.
2012-09-30 | GSE36286 | GEO
Project description:the project aims to provide a glycomic and glycoproteomic approach to reveal S-layer glycosylation on lactobacillus kefiri aggregating and non-aggregating strains
2020-08-24 | PXD020358 | Pride
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
2015-10-15 | GSE56997 | GEO
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with 1.5 mM gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
2015-10-15 | GSE63728 | GEO
Project description:We applied total RNA sequencing of Lactobacillus fermentum strain GR1008 and GR1009 and compare the differentially expressed genes. This study aimed to find out the underlying mechanims for the differential morphology of the two strains.
2022-10-14 | GSE186000 | GEO
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals the induction of genes related to defense mechanisms against oxidative challenge. This response include genes related to inactivation of toxic oxygen radicals, probably derived from the autooxidation of hydroxytyrosol and genes involved in repairing the damage of oxygen radicals on proteins, including those involved in the metabolism of sulphur amino acids. Genes involved in peptidoglycan turnover, strenghthening of the cell wall and genes coding for osmoprotectants transporters, were downregulated. In addition, genes coding for elements typically involved in the stringent response, including ribosomal proteins, enzymes involved in the metabolism of the ppGpp alarmone, nitrogen metabolism, cell division and general stress proteins, were differentially regulated by hydroxytyrosol.
2020-06-17 | GSE90714 | GEO