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

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.

FIG. 1.

Schematic overview of the net expression algorithm.

FIG. 2.

Net expression profiles for the catabolite control protein gene in fermentations D12W, D13W, D12S, and D13S.

FIG. 3.

Relation between the net expression of the maltose phosphorylase gene (black line; right axes) and the concentration of maltose (white bars; left axes) in fermentations D12W, D13W, D12S, and D13S. No data on the maltose concentration were available for time points 120 h, 144 h, 168 h, 192 h, or 216 h for fermentation D12W.

FIG. 4.

Relation between the net expression of the glutamate dehydrogenase gene (black line; right axes) and the branched-chain aminotransferase gene (gray line; right axes) and the production of the branched-chain amino acid metabolites 2-methyl-propanol (black bars; left axes), 2-methyl-butanol (white bars; left axes), and 3-methyl-butanol (shaded bars; left axes) in fermentations D12W, D13W, D12S, and D13S. No data on the concentrations of these alcohols were available for time points 120 h, 144 h, 168 h, 192 h, or 216 h for fermentation D12W. AU, arbitrary units, determined as 100 × [(peak area for compound)/(peak area for internal standard × g of sample)].