Shotgun Metagenomic Approaches

The most recent advancements in the knowledge of sourdough ecologic meta-community come from the uncultured approach based on shotgun metagenomics sequencing and the downstream application of a series of bioinformatics/statistics tools properly concatenated in analytical pipelines. The bioinformatics analysis of raw read sequences has the aim of obtaining a precise quantification of gene annotation and taxonomic assignments. The inspection of this data allows for disclosing the contribution of species into this evolving, heterogeneous, and complex community made by bacteria and yeasts. The comprehensive dataset of taxa and their functional genomic potential is indicative both of metabolic active pathways and possible contaminations due to environmental factors or to human sourdough making processes. A dynamic interplay between major and minor taxa in terms of genomic contribution underlies those processes implying sourdough stability and resilience. In this view, this chapter elucidates concepts related to those taxa identified as mainly responsible for the resilience and robustness of this ecological niche. Moreover, following a theoretical workflow, this chapter provides an up-to date list including the most recent tools commonly used to check read sequence quality, the taxonomic/functional annotation, and the reconstruction of contigs used to infer the completeness of the metabolic pathways fundamental in the maintenance of the functional, organoleptic, and nutritional properties of sourdoughs.