Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1168565 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30877225_1.fastq.gz | Fastqsanger.gz | |||
| SRR30877225_2.fastq.gz | Fastqsanger.gz | |||
| SRR30877226_1.fastq.gz | Fastqsanger.gz | |||
| SRR30877226_2.fastq.gz | Fastqsanger.gz | |||
| SRR30877227_1.fastq.gz | Fastqsanger.gz |
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Project description:In this study, we investigated the transcriptional response of the human isolate L. reuteri ATCC 55730 during sourdough fermentation by using whole-genome microarrays. Significant changes of mRNA levels were found for 101 genes involved in diverse cellular processes, e.g., carbohydrate and energy metabolism, cell envelope biosynthesis, exopolysaccharide production, stress responses, signal transduction and cobalamin biosynthesis. Our results evidence extensive changes of the organism’s gene expression to the growth in sourdough as compared to the growth in chemically defined medium, and thus allowed us to uncover pathways involved in the adaptation of L. reuteri to the ecological niche of sourdough. An impact of several genes of L. reuteri for effective growth in sourdough was shown by implementation of mutant strains in sourdough fermentation. This study contributes to the understanding of the molecular fundamentals of L. reuteri’s ecological competitiveness, and provides a basis for further exploration of genetic traits involved in adaptation to the food and/or intestinal environment. Keywords: environment-specific gene expression, sourdough fermentation, chemically defined medium, dye swap
2008-02-13 | GSE10495 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE15686: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15691: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15692: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) GSE15693: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) Refer to individual Series
2010-07-07 | E-GEOD-15803 | biostudies-arrayexpress
Project description:Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts comes to dominate this ecosystem. Although rich in carbohydrates, thus providing an ideal environment to grow, the low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential growth phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was observed as well as of genes involved in plantaricin production and lipoteichoic acid synthesis. The results highlight cellular mechanisms that allow L. plantarum to function at a low environmental pH.
2011-08-01 | GSE23945 | GEO
Project description:Investigation of the effect of chow diet integration with standard baker's yeast leavened carasau bread (SB) or with functional sourdough-leavened carasau bread (FB) on the gut microbiota of young rats.
2019-08-19 | PXD011441 | Pride
Project description:Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts comes to dominate this ecosystem. Although rich in carbohydrates, thus providing an ideal environment to grow, the low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential growth phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was observed as well as of genes involved in plantaricin production and lipoteichoic acid synthesis. The results highlight cellular mechanisms that allow L. plantarum to function at a low environmental pH. The labeled aRNA samples were hybridized using a loop design, i.e. two consecutive samples (e.g., pH 3.5 and pH 4.0, pH 4.0 and pH 4.5, etc.) were hybridized on the same microarray slide, each labeled with another fluorescent dye (Cy3 or Cy5), and the loop was closed by hybridizing sample pH 5.5 together with sample pH 3.5.
2011-07-31 | E-GEOD-23945 | biostudies-arrayexpress
Project description:The increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effectsof MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad spectrum antimicrobial produced by Limosilactobacillus reuteri and the antibiotic rifampicin were tested for comparison. LC-MS analysis of the cell extracts was used to assess the bacteriocin/antibiotic degradation products and monitor changes in the swine colonic microbiota metabolome.
2021-11-13 | ST002014 | MetabolomicsWorkbench
Project description:Sourdough fermentation, owing to a mixture of yeast and Lactic Acid Bacteria (LAB), is an old biotechnology process that deeply influences the sensory, chemical features and shelf life properties of leavened baked goods. Besides a plethora of functional active metabolites, LABs are able to produce peptides from enzymatic digestion of cereals proteins; which are defined bioactive peptides having important roles in nutrition and healthcare perspective. Starting from the observation that production of peptides is a strain specific feature and that some LAB strains are more efficient in producing Low Molecular Weight peptides, L. farciminis H3 and A11 strains and L. sanfranciscensis I4 strain have been selected for their high ability to produce peptides equipped with biological activity. The peptides isolated from the respective sourdough show antioxidant and anti-inflammatory activity detected as the ability either to reduce intracellular ROS production and to decrease the expression of inflammatory markers like NF-kB and IL-1β in cultured murine macrophages. Herein solid proofs of keeping of the biological activity of the peptides in baked bread are provided to increase the literature data on biological activity in the finished products that is, till now, still scanty. Low Molecular Weight peptides from breads obtained with the LAB strains above mentioned, show the same antioxidant and anti-inflammatory activity as that observed in doughs. Mass spectrometry performed both on doughs and breads highlights a lot of peptides derived from native proteins: among these only three peptides are present in all the analyzed extracts, while a large number of peptides are strain-specific. Moreover, comparing doughs vs breads peptides, major differences can be noticed either in amino acidic composition and in proteins from which they derive. However, irrespective of the sequences, all the tested strains produce bioactive peptides equipped with antioxidant and anti-inflammatory activity
2020-07-21 | PXD013454 | Pride
Project description:In vitro model of digestion and colonic fermentation to investigate consumer chewing differences
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Project description:Changes in microbiome composition have been associated with a wide array of human diseases, turning the human microbiota into an attractive target for therapeutic intervention. Yet clinical translation of these findings requires the establishment of causative connections between specific microbial taxa and their functional impact on host tissues. Here, we infused gut organ cultures with longitudinal microbiota samples collected from therapy-naïve irritable bowel syndrome (IBS) patients under low-FODMAP (fermentable Oligo-, Di-, Mono-saccharides and Polyols) diet. We show that post-diet microbiota regulates intestinal expression of inflammatory and neuro-muscular gene-sets. Specifically, we identify Bifidobacterium adolescentis as a diet-sensitive pathobiont that alters tight junction integrity and disrupts gut barrier functions. Collectively, we present a unique pathway discovery approach for mechanistic dissection and identification of functional diet-host-microbiota modules. Our data support the hypothesis that the gut microbiota mediates the beneficial effects of low-FODMAP diet and reinforce the potential feasibility of microbiome based-therapies in IBS.
2022-10-14 | GSE215049 | GEO