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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of natural wheat and spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation

ABSTRACT: 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

ORGANISM(S): Lactobacillus paracasei

SUBMITTER: Joke Allemeersch

PROVIDER: E-GEOD-15803 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Community dynamics of bacteria in sourdough fermentations as revealed by their metatranscriptome.

Weckx Stefan S Van der Meulen Roel R Allemeersch Joke J Huys Geert G Huys Geert G Vandamme Peter P Van Hummelen Paul P De Vuyst Luc L

Applied and environmental microbiology 20100625 16

The lactic acid bacterial (LAB) community dynamics of two wheat and two spelt sourdough fermentations that were daily back-slopped were monitored during a period of 10 days by hybridizing time-related RNA samples, representing the metatranscriptome, to an LAB functional gene microarray. To indicate the species present in each hybridized sample, annotation information for the 2,269 oligonucleotides on the microarray was used. The overall hybridization data revealed that after a transition phase o ...[more]

PMID: 20581179

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Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation

Project description:Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level. The labeled aRNA of the sourdough fermentation samples was hybridized using a loop design, i.e. subsequent samples (e.g. 27 h and 51 h, 51 h and 75 h etc.) were hybridized together on the microarray and the loop was closed by hybridizing the last sample with the first.

2010-07-07 | E-GEOD-15693 | biostudies-arrayexpress

Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

2010-07-07 | E-GEOD-15686 | biostudies-arrayexpress

Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, adapts to growth in wheat sourdough simulation medium at different pH values through differential gene expression

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

PgGenExpress database of transcription profiles

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2012-02-08 | E-GEOD-35624 | biostudies-arrayexpress

Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation

Project description:Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation

| PRJNA123017 | ENA

Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation

Project description:Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation

| PRJNA123013 | ENA

Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation.

Project description:Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation.

| PRJNA123015 | ENA

Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

Project description:Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

| PRJNA123009 | ENA

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Project description:The goal of this experiment is to evaluate the potential for utilising this oligonucleotide microarray in other species and genera of the Pinaceae family by using comparative RNA hybridizations in four different spruces (Picea spp), two pines (Pinus spp.) and a larch (Larix laricina), across two tissues, xylem and phelloderm. One-color comparison of 7 conifer species in 2 tissue types: xylem and phelloderm. Between 4 and 28 biological repetitions per sample type, depending on the species, for a total of 142 slides.

2012-02-16 | E-GEOD-35847 | biostudies-arrayexpress

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2012-02-18 | E-GEOD-35922 | biostudies-arrayexpress

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