From Wild Strain to Domesticated Strain: The Philosophy of Microbial Diversity in Foods

Abstract

In context with “the different and contrasting roles of microorganisms in food quality, shelf life, and safety” (Guerzoni, 2010), the knowledge on how wild strains become domesticated represents a common research priority for food microbiologists. The diversity of microbial communities and their ecological and metabolic functions have the potential for remarkable scientific, social, and economic impact. However, microbiological diversity remains largely undiscovered and the knowledge of its global distribution and temporal variability remain elusive. The biosphere is estimated to contain between 1030 and 1031 different microbial genomes; however, we likely only know a minority of them at present (Whitman et al., 1998). Sequencing surveys of amplified regions of small subunit ribosomal RNA (SSU rRNA) genes have revealed that microbial diversity is much greater than the 5,000 microbial species described using phenotypic features in Bergey's taxonomic outline (Staley, 2006), and that microbial communities are far more complex than initially thought. Hence the application of molecular phylogenetic methods to study natural microbial ecosystems has resulted in the unexpected discovery of many evolutionary lineages. In addition, the recent surge of research in molecular microbial ecology produced compelling evidence for the existence of many novel types of microorganisms in the environment – both regarding abundance and diversity – that dwarf those of the comparatively few microorganisms amenable to laboratory cultivation. Collectively, the genomes of the total microbiota found in nature, termed the metagenome (Sebat et al., 2003; Handelsman, 2004), contain vastly more genetic information than is contained in the culturable subset. Comparative genomics, gaining a better understanding of how species have evolved, has shown the power to determine the function of genes and non-coding regions of the genome. The comparative genomics of the lactic acid bacteria reported by Makarova et al. (2006), for instance, demonstrated the phylogenetic and functional diversity of these bacteria. The reconstruction of ancestral gene sets revealed a combination of gene loss and gain during coevolution of lactic acid bacteria with animals and the foods they consumed. The study proposed that the origin of Lactobacillales involved extensive loss of ancestral genes (600–1200 genes) during their transition to life in a nutritionally rich medium, which allowed a reduction in catabolic capacity and an increased stress resistance.