Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

Abstract

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.

Oral Lactobacilli and Dental Caries

“…The phylogenetic relationships and taxonomy of the Lactobacillus genus have been complicated by this loss or replacement of large segments of their genomes. The most recent phylogenetic reconstruction revealed that Lactobacillus is paraphyletic and that 5 other genera are grouped within the lactobacilli as subclades (Sun et al 2014).…”

“…Niche-specific genes have been identified in Lactobacillus species associated with dairy and gut environments (O'Sullivan et al 2009). On the other hand, the search for common niche-specific genetic loci for vaginal Lactobacillus species remains unresolved (Ravel et al 2011) despite their close phylogenetic relationships (Salvetti 2012;Sun et al 2014). …”

Metabolism and physiology of Lactobacilli: a review

“…These lost genes, particularly related to cofactor biosynthesis and sporulation, are indicative of the shift to a more nutrient-rich environment (Makarova et al, 2006). Currently, it is known that Lactobacillus genome size varies from 1.23 Mb (L. sanfranciscensis) to 4.91 Mb (L. parakefiri) (Sun et al, 2015).…”

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

“…WGS has provided invaluable insights into the genetics of starter cultures (2,3), and it is routinely used in epidemiology to identify outbreak-associated foodborne pathogens isolated from clinical samples, through comparison of the single-nucleotide polymorphism (SNP) profiles of outbreak strain genomes versus nonoutbreak strain genomes (4)(5)(6). Metagenomic sequencing enables elucidation of the roles of microorganisms during food production (7)(8)(9), and it can be used to track microorganisms of interest through the food production chain, as illustrated by Yang et al (10), who used whole-metagenome shotgun sequencing to track pathogenic species in the beef production chain.…”