Lactobacillus salivarius genome sequencing
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REPOSITORIES: ENA
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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
Project description:Porcine bile induced transcriptome of Lactobacillus salivarius
2009-07-16 | E-MEXP-2224 | biostudies-arrayexpress
Project description:bile induced transcriptome of Lactobacillus salivarius LS201bsh ko.
2009-07-17 | E-MEXP-2225 | biostudies-arrayexpress
Project description:Lactobacillus salivarius TUCO-L2 genome sequencing and assembly
| PRJEB31615 | ENA
Project description:Lactobacillus helveticus is a rod-shaped lactic acid bacterium that is widely used in the manufacture of fermented dairy foods and for production of bioactive peptides from milk proteins. Although L. helveticus is commonly associated with milk environments, phylogenetic studies show it is closely related to an intestinal species, Lactobacillus acidophilus, which has been shown to impart probiotic health benefits to humans. This relationship has fueled a prevailing hypothesis that L. helveticus is a highly specialized derivative of L. acidophilus which has adapted to acidified whey. However, L. helveticus has also been sporadically recovered from non-dairy environments, which argues the species may not be as highly specialized as is widely believed. This study employed genome sequence analysis and comparative genome hybridizations to investigate genomic diversity among L. helveticus strains collected from cheese, whey, and whiskey malt, as well as commercial cultures used in manufacture of cheese or bioactive dairy foods. Results revealed considerable variability in gene content between some L. helveticus strains, and indicated the species should not be viewed as a strict dairy-niche specialist. In addition, comparative genomic analyses provided new insight on several industrially and ecologically important attributes of L. helveticus that may facilitate commercial strain selection.
2013-08-16 | GSE23660 | GEO
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
Project description:Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences of L. salivarius BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate.
| S-EPMC5701484 | biostudies-literature
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.
2017-08-01 | GSE92837 | GEO
Project description:Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of L. salivarius are recognized, salivarius and salicinius, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in L. salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments.
| S-EPMC1436024 | biostudies-literature
Project description:In the present study we characterized the sRNA profile of Lactobacillus casei BL23 using conventional and mDOT-seq approaches. In total 307 potential sRNAs were identified, 28 of which were validated by Northern hybridization. As a major portion of predicted sRNAs were shown to be conserved among the related species of Lactobacillus casei group (LCG), the results obtained in this study could serve as a valuable resource for achieving a better understanding of LCG physiology or even improving their applications in industry and medicine.
2021-05-20 | GSE166930 | GEO