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Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations

Stefan Weckx, Joke Allemeersch, Roel Van der Meulen, Gino Vrancken, Geert Huys, Peter Vandamme UGent, Paul Van Hummelen and Luc De Vuyst (2011) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 77(2). p.618-626
abstract
Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during the last decade, transcriptome and, by extension, metatranscriptome studies have become one of the most appropriate research approaches to study whole-ecosystem gene expression in more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory with an in-house-developed LAB functional gene microarray. For data analysis, a new algorithm was developed to calculate a net expression profile for each of the represented genes, allowing use of the microarray analysis beyond the species level. In addition, metabolite target analyses were performed on the sourdough samples to relate gene expression with metabolite production. The results revealed the activation of different key metabolic pathways, the ability to use carbohydrates other than glucose (e.g., starch and maltose), and the conversion of amino acids as a contribution to redox equilibrium and flavor compound generation in LAB during sourdough fermentation.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
LACTIC-ACID BACTERIA, COMPLETE GENOME SEQUENCE, LACTOCOCCUS-LACTIS, LACTOBACILLUS-PLANTARUM, TRANSCRIPTIONAL RESPONSE, CATABOLITE REPRESSION, MICROARRAY ANALYSIS, PROTEOLYTIC SYSTEM, COMMUNITY DYNAMICS, FLAVOR FORMATION
journal title
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
Appl. Environ. Microbiol.
volume
77
issue
2
pages
618 - 626
Web of Science type
Article
Web of Science id
000286147300029
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
3.829 (2011)
JCR rank
29/157 (2011)
JCR quartile
1 (2011)
ISSN
0099-2240
DOI
10.1128/AEM.02028-10
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1203943
handle
http://hdl.handle.net/1854/LU-1203943
date created
2011-04-06 17:19:56
date last changed
2016-12-19 15:45:49
@article{1203943,
  abstract     = {Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during the last decade, transcriptome and, by extension, metatranscriptome studies have become one of the most appropriate research approaches to study whole-ecosystem gene expression in more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory with an in-house-developed LAB functional gene microarray. For data analysis, a new algorithm was developed to calculate a net expression profile for each of the represented genes, allowing use of the microarray analysis beyond the species level. In addition, metabolite target analyses were performed on the sourdough samples to relate gene expression with metabolite production. The results revealed the activation of different key metabolic pathways, the ability to use carbohydrates other than glucose (e.g., starch and maltose), and the conversion of amino acids as a contribution to redox equilibrium and flavor compound generation in LAB during sourdough fermentation.},
  author       = {Weckx, Stefan and Allemeersch, Joke and Van der Meulen, Roel and Vrancken, Gino and Huys, Geert and Vandamme, Peter and Van Hummelen, Paul and De Vuyst, Luc},
  issn         = {0099-2240},
  journal      = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
  keyword      = {LACTIC-ACID BACTERIA,COMPLETE GENOME SEQUENCE,LACTOCOCCUS-LACTIS,LACTOBACILLUS-PLANTARUM,TRANSCRIPTIONAL RESPONSE,CATABOLITE REPRESSION,MICROARRAY ANALYSIS,PROTEOLYTIC SYSTEM,COMMUNITY DYNAMICS,FLAVOR FORMATION},
  language     = {eng},
  number       = {2},
  pages        = {618--626},
  title        = {Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations},
  url          = {http://dx.doi.org/10.1128/AEM.02028-10},
  volume       = {77},
  year         = {2011},
}

Chicago
Weckx, Stefan, Joke Allemeersch, Roel Van der Meulen, Gino Vrancken, Geert Huys, Peter Vandamme, Paul Van Hummelen, and Luc De Vuyst. 2011. “Metatranscriptome Analysis for Insight into Whole-ecosystem Gene Expression During Spontaneous Wheat and Spelt Sourdough Fermentations.” Applied and Environmental Microbiology 77 (2): 618–626.
APA
Weckx, Stefan, Allemeersch, J., Van der Meulen, R., Vrancken, G., Huys, G., Vandamme, P., Van Hummelen, P., et al. (2011). Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 77(2), 618–626.
Vancouver
1.
Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, Huys G, Vandamme P, et al. Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2011;77(2):618–26.
MLA
Weckx, Stefan, Joke Allemeersch, Roel Van der Meulen, et al. “Metatranscriptome Analysis for Insight into Whole-ecosystem Gene Expression During Spontaneous Wheat and Spelt Sourdough Fermentations.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 77.2 (2011): 618–626. Print.