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

ABSTRACT: 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.

ORGANISM(S): Lacticaseibacillus casei Companilactobacillus farciminis Limosilactobacillus panis Weissella confusa Lactobacillus helveticus Latilactobacillus curvatus Pediococcus pentosaceus Lentilactobacillus hilgardii Lactococcus lactis Enterococcus mundtii Lentilactobacillus buchneri Streptococcus thermophilus Lactobacillus gasseri Brevibacterium linens Limosilactobacillus pontis Lactobacillus crispatus Lactobacillus acidophilus Fructilactobacillus sanfranciscensis Latilactobacillus sakei Companilactobacillus alimentarius Lactiplantibacillus pentosus Enterococcus faecium Lactobacillus delbrueckii Bifidobacterium Lacticaseibacillus paracasei Oenococcus oeni Fructilactobacillus fructivorans Lentilactobacillus parabuchneri Companilactobacillus mindensis Leuconostoc mesenteroides Lactiplantibacillus plantarum Companilactobacillus paralimentarius Lacticaseibacillus rhamnosus Furfurilactobacillus rossiae Limosilactobacillus fermentum Enterococcus faecalis Leuconostoc pseudomesenteroides Mammaliicoccus lentus Enterococcus casseliflavus Leuconostoc citreum Lactiplantibacillus paraplantarum Lactobacillus johnsonii Pediococcus acidilactici Lactobacillus amylovorus Staphylococcus aureus Enterococcus hirae Limosilactobacillus reuteri Levilactobacillus brevis Limosilactobacillus frumenti

PROVIDER: GSE15693 | GEO | 2010/07/07

SECONDARY ACCESSION(S): PRJNA123017

REPOSITORIES: GEO