Metagenomic of Kefir-UDI strain
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ABSTRACT:
PROVIDER: PRJEB40661 | ENA |
REPOSITORIES: ENA
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Project description:This project aimed to explore the microbial chemical ecology of a consortium derived from a water kefir fermentation through the integration of directed culturomics, compositional metagenomics and the identification of key metabolites with biological potential, through untargeted metabolomics.
2023-05-15 | MSV000091955 | MassIVE
Project description:We got insights into the B. bifidum PRL2010 genes whose expression resulted to be affected when bacterial cells were cultivated on kefir and kefiran as the unique carbon source.
2016-01-01 | GSE50506 | GEO
Project description:Shotgun metagenomic analysis of traditional kefir from Caucasus
| PRJEB111907 | ENA
Project description:We got insights into the B. bifidum PRL2010 genes whose expression resulted to be affected when bacterial cells were cultivated on kefir and kefiran as the unique carbon source. In order to exploit the transcriptome of PRL2010 grown on kefir and hefiran we performed global transcription profiling using PRL2010 microarrays hybridized with cDNA from the RNA samples of B. bifidum PRL2010 cultivated on these substrates. We isolated mRNA from B. bifidum PRL2010 cells collected from a culture of kefir grains and from PRL2010 cultivated on MRS plus kefiran at upon 12 hours following inoculation. Microarray analysis was performed with an oligonucleotide array based on the B. bifidum PRL2010 genome: a total of 8,130 oligonucleotide probes of 60bp in length were designed on 1707 ORFs using eArray5.0 (Agilent Technologies). 5 Oligos were designed for each gene on a 4x44k Agilent Microarrays(Agilent Technologies, Santa Clara, CA, USA). Replicates were distributed on the chip at random, non-adjacent positions.
2016-07-03 | E-GEOD-50506 | biostudies-arrayexpress
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress
Project description:This project aimed to explore the microbial chemical ecology of a consortium derived from a water kefir fermentation through the integration of directed culturomics, compositional metagenomics and the identification of key metabolites with biological potential, through untargeted metabolomics.
2023-05-15 | MSV000091955 | GNPS
Project description:Metagenomic characterization of Chilean kefir beverages
| PRJEB38902 | ENA
Project description:Objective: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD. Design: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alter the course of acute dextran sodium sulfate (DSS) colitis. Rag1-/- and Gpr15-/- mice were used to investigate the role of T cells and Gpr15 for Gpr15l-dependent effects in acute DSS and T cell transfer colitis, respectively. The impact of GPR15L on microbiota was explored with co-housing, littermate and fecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and anaerobic cultures of human stool suspensions analyzed by shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival. Results: Gpr15l clearly mitigated experimental colitis, but this was independent of T cell recruitment and Gpr15. Instead, we observed that the effects of Gpr15l were mediated by altered microbiomes in the large intestine and, consistently, showed that Gpr15l acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of Gpr15l counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival. Conclusions: GPR15L is a host-defense peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.
2026-05-26 | GSE328435 | GEO