Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequences of Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, Isolated from a Beetroot Product.

ABSTRACT: Lactic acid bacteria (LAB) participate in fermentation processes and have probiotic potential. The genomes of three LAB strains, Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei subsp. paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, isolated from a beetroot product, were characterized. The results contribute to our understanding of the beneficial properties of LAB.

SUBMITTER: Kaszab E

PROVIDER: S-EPMC8759371 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparison of R1, R2 and R3

Project description:3 samples of R1, R2 and R3 bone marrow monocytes were compared from 3 biological replicates in 3 separate experiments. R1, R2 and R3 were sorted from triplicate experiments from pools of mice

2016-11-24 | GSE90471 | GEO

Sludge(R1-AGS/R2-AGB/R3-eAGB/R3-iAGB)

Project description:Sludge(R1-AGS/R2-AGB/R3-eAGB/R3-iAGB) Raw sequence reads

| PRJNA1155813 | ENA

Effect of Inoculation with Lentilactobacillus buchneri and Lacticaseibacillus paracasei on the Maize Silage Volatilome: The Advantages of Advanced 2D-Chromatographic Fingerprinting Approaches.

Project description:In this study, the complex volatilome of maize silage samples conserved for 229 d, inoculated with Lentilactobacillus buchneri (Lbuc) and Lacticaseibacillus paracasei (Lpar), is explored by means of advanced fingerprinting methodologies based on comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry. The combined untargeted and targeted (UT) fingerprinting strategy covers 452 features, 269 of which were putatively identified and assigned within their characteristic classes. The high amounts of short-chain free fatty acids and alcohols were produced by fermentation and led to a large number of esters. The impact of Lbuc fermentation was not clearly distinguishable from the control samples; however, Lpar had a strong and distinctive signature that was dominated by propionic acid and 1-propanol characteristic volatiles. The approach provides a better understanding of silage stabilization mechanisms against the degradative action of yeasts and molds during the exposure of silage to air.

| S-EPMC9523707 | biostudies-literature

Anti-Inflammatory Response in TNFα/IFNγ-Induced HaCaT Keratinocytes and Probiotic Properties of Lacticaseibacillus rhamnosus MG4644, Lacticaseibacillus paracasei MG4693, and Lactococcus lactis MG5474.

Project description:Atopic dermatitis (AD) is a chronic inflammatory disease caused by immune dysregulation. Meanwhile, the supernatant of lactic acid bacteria (SL) was recently reported to have anti-inflammatory effects. In addition, HaCaT keratinocytes stimulated by tumor necrosis factor alpha (TNF-α) and interferon gamma (IFN-γ) are widely used for studying AD-like responses. In this study, we evaluated the anti-inflammatory effects of SL from lactic acid bacteria (LAB) on TNF-α/IFN-γ-induced HaCaT keratinocytes, and then we investigated the strains' probiotic properties. SL was noncytotoxic and regulated chemokines (macrophage-derived chemokine (MDC) and thymus and activation-regulated chemokine (TARC)) and cytokines (interleukin (IL)-4, IL-5, IL-25, and IL-33) in TNF-α/IFN-γ-induced HaCaT keratinocytes. SL from Lacticaseibacillus rhamnosus MG4644, Lacticaseibacillus paracasei MG4693, and Lactococcus lactis MG5474 decreased the phosphorylation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK). Furthermore, the safety of the three strains was demonstrated via hemolysis, bile salt hydrolase (BSH) activity, and toxicity tests, and the stability was confirmed under simulated gastrointestinal conditions. Therefore, L. rhamnosus MG4644, L. paracasei MG4693, and Lc. lactis MG5474 have potential applications in functional food as they are stable and safe for intestinal epithelial cells and could improve atopic inflammation.

| S-EPMC10468673 | biostudies-literature

Genome Sequence of Lacticaseibacillus rhamnosus Strain NCDC610, Isolated from a Traditional Cereal-Based Fermented Milk Product (Raabadi).

Project description:We announce the draft genome sequence of Lacticaseibacillus rhamnosus NCDC610, an isolate from an Indian traditional cereal-based fermented milk product (Raabadi). The genome size of Lacticaseibacillus rhamnosus NCDC610 is 2.91 Mb with the assembled sequence, and the genome consists of 67 contigs.

| S-EPMC8582304 | biostudies-literature

Complete Genome Sequence of Lacticaseibacillus paracasei Strain NSMJ15.

Project description:We report here the complete genome sequence of Lacticaseibacillus paracasei NSMJ15, isolated from makgeolli (a traditional Korean fermented liquor) and shown to have potentially probiotic characteristics. The genome consisted of a 2.79-Mbp chromosome contig and four plasmids having a total of 2,947 genes, including 2,690 coding sequences.

| S-EPMC8656385 | biostudies-literature

Functional characterization and transcriptional repression by Lacticaseibacillus paracasei DinJ-YafQ.

Project description:DinJ-YafQ is a bacterial type II TA system formed by the toxin RNase YafQ and the antitoxin protein DinJ. The activity of YafQ and DinJ has been rigorously studied in Escherichia coli, but little has been reported about orthologous systems identified in different microorganisms. In this work, we report an in vitro and in vivo functional characterization of YafQ and DinJ identified in two different strains of Lacticaseibacillus paracasei and isolated as recombinant proteins. While DinJ is identical in both strains, the two YafQ orthologs differ only for the D72G substitution in the catalytic site. Both YafQ orthologs digest ribosomal RNA, albeit with different catalytic efficiencies, and their RNase activity is neutralized by DinJ. We further show that DinJ alone or in complex with YafQ can bind cooperatively to a 28-nt inverted repeat overlapping the -35 element of the TA operon promoter. Atomic force microscopy imaging of DinJ-YafQ in complex with DNA harboring the cognate site reveals the formation of different oligomeric states that prevent the binding of RNA polymerase to the promoter. A single amino acid substitution (R13A) within the RHH DNA-binding motif of DinJ is sufficient to abolish DinJ and DinJ-YafQ DNA binding in vitro. In vivo experiments confirm the negative regulation of the TA promoter by DinJ and DinJ-YafQ and unveil an unexpected high expression-related toxicity of the gfp reporter gene. A model for the binding of two YafQ-(DinJ)2-YafQ tetramers to the promoter inverted repeat showing the absence of protein-protein steric clash is also presented. KEY POINTS: • The RNase activity of L. paracasei YafQ toxin is neutralized by DinJ antitoxin. • DinJ and DinJ-YafQ bind to an inverted repeat to repress their own promoter. • The R13A mutation of DinJ abolishes DNA binding of both DinJ and DinJ-YafQ.

| S-EPMC9592637 | biostudies-literature

Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei.

Project description:Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The distribution of 6mA-modified sites varies across the genomes of 28 strains, and appears to be enriched near genes involved in carbohydrate metabolism. A pglX mutant, defective in 6mA modification, shows transcriptomic alterations but only modest changes in growth and genomic spatial organization.

| S-EPMC10164179 | biostudies-literature

R1,R2 granules

Project description:R1,R2 granules Raw sequence reads

| PRJNA1057446 | ENA

Elemental sulfur enhances the anti-fungal effect of Lacticaseibacillus rhamnosus Lcr35

Project description:Lacticaseibacillus rhamnosus Lcr35 is a well-known bacterial strain whose efficiency in preventing recurrent vulvovaginal candidiasis has been largely demonstrated in clinical trials. The presence of sodium thiosulfate (STS) has been shown to enhance its ability to inhibit the growth of C. albicans strains. In this study, we confirmed that Lcr35 has a fungicidal effect not only on the planktonic form of C. albicans but also on other life forms such as hypha and biofilm. Transcriptomic analysis showed that the presence of C. albicans induced a metabolic adaptation of Lcr35 potentially associated with a competitive advantage over yeast cells. However, STS alone had no impact on the global gene expression of Lcr35, which is not in favor of the involvement of an enzymatic transformation of STS. Comparative gas chromatography- mass spectrometry analysis of the organic phase from cell-free supernatant (CFS) fractions obtained from Lcr35 cultures performed in the presence and absence of STS identified elemental sulfur (S0) in the samples initially containing STS. In addition, the anti-candida activity of CFS from STS-containing cultures was shown to be pH-dependent and occurred at acidic pH lower than 5. We next investigated the antifungal activity of lactic acid and acetic acid, the two main organic acids produced by Lactobacillus spp. The two molecules affected the viability of C. albicans but only at pH 3.5 and in a dose-dependent manner, an antifungal effect that was enhanced in samples containing STS in which the thiosulfate was decomposed into S0. In conclusion, the use of STS as an excipient in the manufacturing process of Lcr35 exerted a dual action since the production of organic acids by Lcr35 facilitates the decomposition of thiosulfate into S0, thereby enhancing the bacteria’s own anti-fungal effect.

2024-01-08 | GSE242938 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data