Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA513828 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR8418875_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR8422046_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR8466611_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR8476696_subreads.fastq.gz | Fastqsanger.gz |
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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:This project analyzed the proteomics of extracellular vesicles of kefir derived lactic acid bacteria. Samples were analyzed on timsTOF Pro (Bruker Daltonics), a hybrid trapped ion mobility spectrometer (TIMS) quadrupole time-of-flight mass spectrometer. The functional characteristics of extracellular vesicles of kefir derived lactic acid bacteria were obtained through bioinformatics analysis
2025-10-13 | PXD069374 |
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:Kefir is a milk fermented by microorganisms with probiotic potential. Its consumption is associated with several beneficial effects, from antibacterial, healing, antioxidant, anti-inflammatory, anti-allergic, plasma glucose and cholesterol control to antitumor and antihypertensive activities. Despite its great potential, little is known about the bioactive molecules responsible for these actions. Therefore, the present project aims to perform the proteomic study of Kefir and its grain used for the milk fermentation aiming to identify the bioactive peptides, in particular those peptides with action in the cardiovascular system.
2019-12-16 | PXD012074 | JPOST Repository
Project description:Humans and microorganisms, both symbiotic and pathogenic, have evolved means to communicate through the dissemination of biological signals. In addition to small molecules and proteins, mobile small RNAs (sRNAs) have recently emerged as signal molecules that mediate inter-species crosstalk by functional RNA interference (RNAi). However, the trafficking of sRNAs between humans and microorganisms, as well as the resulting biological consequences, remains unexplored. Here, we report that human cells secrete exosomes to deliver sRNAs into bacteria and induce bacterial gene silencing. The unprecedented RNAi in bacteria is accomplished primarily through translational repression without mRNA degradation, for which the participation of human AGO2 proteins co-transferred with sRNAs is essential. Exosome-mediated bacterial RNAi was further applied to fight superbug infection by targeting drug-resistance genes in a mouse model. Our discovery of this unique exosome-mediated sRNA delivery and gene silencing in bacteria paves the way to understanding and manipulating the cross-kingdom communication between human hosts and intestinal microbiota, as well as between humans and pathogenic bacteria.
2025-03-06 | GSE122212 | GEO
Project description:The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium Lb. bulgaricus . S. cerevisiae and Lb. bulgaricus are both frequently encountered in kefir, a fermented dairy product (25). In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together (19,26-30). The design of the cultivation conditions was based on the observation that Lb. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not Lb. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial M-NM-2-galactosidase. Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. Lb. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, Lb. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. bulgaricus. 5. Transcriptome analysis of Lb. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae. To our knowledge, this is the first transcriptome study of a cross-kingdom binary mixed culture that analyses responses of both microorganisms. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigated microbial interaction in mixed populations. To investigate the impact of of co-cultivation with Lb. bulgaricus on S. cerevisiae, a DNA microarray-based transcriptome analysis of S. cerevisiae's response was performed on anaerobic, lactose-limited chemostat cultures grown in the presence and absence of L. bulgaricus.
2013-08-22 | E-GEOD-45776 | biostudies-arrayexpress
Project description:The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium L. bulgaricus . S. cerevisiae and L. bulgaricus are both frequently encountered in kefir, a fermented dairy product. In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together. The design of the cultivation conditions was based on the observation that L. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not L. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial β-galactosidase. Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. L. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by L. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, L. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by L. bulgaricus. 5. Transcriptome analysis of L. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae.
2013-04-01 | GSE45623 | GEO
Project description:The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium Lb. bulgaricus . S. cerevisiae and Lb. bulgaricus are both frequently encountered in kefir, a fermented dairy product (25). In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together (19,26-30). The design of the cultivation conditions was based on the observation that Lb. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not Lb. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial β-galactosidase. Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. Lb. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, Lb. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. bulgaricus. 5. Transcriptome analysis of Lb. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae. To our knowledge, this is the first transcriptome study of a cross-kingdom binary mixed culture that analyses responses of both microorganisms. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigated microbial interaction in mixed populations.
2013-08-22 | GSE45776 | GEO