Similar Datasets
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: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:<p>Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realises stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.</p><p><br></p><p><strong>Linked metabolomics studies:</strong></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1829' rel='noopener noreferrer' target='_blank'>MTBLS1829</a> Kefir fermentation curve (FIA-MS)</p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1830' rel='noopener noreferrer' target='_blank'>MTBLS1830</a> Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)</p><p><br></p><p><strong>Linked cross omic data:</strong></p><p>Genomes of isolated kefir species are available in the <a href='https://www.ncbi.nlm.nih.gov/' rel='noopener noreferrer' target='_blank'>NCBI database</a> under the accession: PRJNA375758 (bioproject ID: 375758).</p><p>Metatranscriptomic sequencing reads can be accessed from <a href='www.ebi.ac.uk/ena' rel='noopener noreferrer' target='_blank'>ENA</a> under the project id PRJEB37001.</p><p>Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.</p>
2020-11-04 | MTBLS1823 | MetaboLights
Project description:This study examines the proteolytic activity of the kefir grains (a combination of bacteria and yeast) on bovine milk proteins. SDS-PAGE analysis reveals substantial digestion of milk proteins by the kefir grains in comparison with control samples. Mass spectrometric analysis reveals that the kefir microorganisms released 609 new peptide fragments and significantly altered the abundance of around 1,500 peptides compared to the controls. These kefir-digested peptides derived from 55 milk proteins. We show that kefir contains 25 previously identified functional peptides with actions including antihypertensive, antimicrobial, opioid and anti-oxidative .
2016-05-09 | PXD001826 | Pride
Project description:<p>Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realises stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.</p><p><br></p><p><strong>Linked metabolomics studies:</strong></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1823' rel='noopener noreferrer' target='_blank'>MTBLS1823</a> Spent-medium assay, measured untargeted (FIA-qTOF) and targeted (HILIC, LC-MS)</p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1830' rel='noopener noreferrer' target='_blank'>MTBLS1830</a> Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)</p><p><br></p><p><strong>Linked cross omic data sets:</strong></p><p>Genomes of isolated kefir species are available in the NCBI database under the accession: PRJNA375758 (bioproject ID: 375758).</p><p>Metatranscriptomic sequencing data associated with this study are available in the European Nucleotide Archive (ENA): accession number <a href='https://www.ebi.ac.uk/ena/browser/view/PRJEB37001' rel='noopener noreferrer' target='_blank'>PRJEB37001</a>.</p><p>Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.</p>
2020-11-04 | MTBLS1829 | MetaboLights
Project description:Interventions: Kefir intake group(4 to 12 weeks)
Kefir long-term intake group (5 years)
Non-intake group
Primary outcome(s): Changes of the oral flora and intestinal flora Changes in the immune markers such as cell-mediated immunity Response Evaluation Criteria in Solid Tumors Overall survival time, Progression-free survival
Study Design: Parallel Randomized
| 2639154 | ecrin-mdr-crc