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

• DOI: 10.1038/ncomms9322
• Publication Date: 2015-09-29T10:07:29Z
• Authors: Zhihong Sun; Hugh M. B. Harris; Angela McCann; Chenyi Guo; Silvia Argimón; Wenyi Zhang; Xianwei Yang; Ian B Jeffery; Jakki C. Cooney; Todd F. Kagawa; Wenjun Liu; Yuqin Song; Elisa Salvetti; Agnieszka Wrobel; Pia Rasinkangas; Julian Parkhill; Mary C. Rea; Orla O’Sullivan; Jarmo Ritari; François P. Douil...; R. Paul Ross; Ruifu Yang; Alexandra E. Briner; Giovanna E. Felis; Willem M. de Vos; Rodolphe Barrangou; Todd R. Klaenhammer; Page W. Caufield; Yujun Cui; Heping Zhang; Paul W. O’Toole
• Keywords: 0301 basic medicine; GRAM-POSITIVE BACTERIA; PROTEIN; LACTIC-ACID BACTERIA; Article; MULTIPLE SEQUENCE ALIGNMENT; Veterinary science; 03 medical and health sciences; CRISPR-CAS SYSTEMS; Life Science; PHYLOGENETIC ANALYSIS; Pediococcus; Phylogeny; 2. Zero hunger; MOLECULAR-CLONING; GENUS LACTOBACILLUS; GLYCOSIDE HYDROLASE FAMILY; Sequence Analysis, DNA; PROBIOTICS; 3. Good health; Lactobacillus; Lactobacillus, comparative genomics, biotechnology; Genome, Bacterial; Leuconostoc; Biotechnology

AbstractLactobacilli 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.