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Omics approaches to understand sourdough fermentation processes

Weckx, Stefan, Van Kerrebroeck, Simon, De Vuyst, Luc
International journal of food microbiology 2019 v.302 pp. 90-102
DNA, automation, databases, fermentation, genes, lactic acid bacteria, metabolites, metagenomics, microarray technology, sourdough, terminology, transcriptomics, yeasts
The application of omics methodologies helps to further unravel sourdough fermentation processes. Of all methodologies applied, metagenetics is the most used one to analyse sourdoughs, allowing to elucidate their microbial structure, albeit that it is based on the sequencing of a very small part of whole-community DNA. Although shotgun metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics are very promising to analyse sourdough fermentations and the terminology is often used in a confusing way, they have not been fully used sensu stricto yet. For instance, up to now, metatranscriptomics is restricted to the use of a functional gene microarray for lactic acid bacteria. Further, meta-metabolomics often deals with metabolite target analysis of sourdough fermentation samples to determine the actual concentrations of residual substrates and metabolites produced as well as to list their volatilome solely. In contrast, genomics has been applied several times, albeit that the whole-genome sequence of only one yeast strain and of 41 lactic acid bacterial strains, originally isolated from sourdoughs, is available. However, the genomics data accessible in public databases should be considered with caution because of inaccurate gene annotations, due to automated annotation pipelines, thereby possibly overruling original, high-quality, well-curated gene annotations.