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

TLDR

Lactobacilli are diverse species used in biotechnology, food preservation, and therapeutics, yet their metabolic diversity, unclear species identity, and relationships to other lactic acid bacteria hinder exploitation of their untapped biotransformation potential. This study reports genome sequences of 213 Lactobacillus strains and related genera, cataloguing genes for carbohydrate and protein modification, novel CRISPR‑Cas systems, host interaction factors, and bacteriocins, and establishes a phylogenomic framework for species classification. The authors sequenced the genomes, identified genetic determinants of carbohydrate and protein modification, CRISPR‑Cas immunity, host interaction, and bacteriocin production, and used phylogenomic analysis to classify existing and new species.

Abstract

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.