Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation
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PROVIDER: PRJNA123009 | ENA |
REPOSITORIES: ENA
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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: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
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-15686 | biostudies-arrayexpress
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.
2010-07-07 | GSE15686 | GEO
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.
2010-07-07 | GSE15693 | GEO
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.
2010-07-07 | GSE15692 | GEO
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.
2010-07-07 | GSE15691 | GEO
Project description:Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation
| PRJNA123017 | ENA
Project description:Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation
| PRJNA123013 | ENA
Project description:Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation.
| PRJNA123015 | ENA