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Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
Sun, Zhihong; Harris, Hugh M. B.; McCann, Angela; Guo, Chenyi; Argimon, Silvia; Zhang, Wenyi; Yang, Xianwei; Jeffrey, Ian B.; Cooney, Jakki C.; Kagawa, Todd F.; Liu, Wenjun; Song, Yuqin; Salvetti, Elisa; Wrobel, Agneszka; Rasinkangas, Pia; Parkhill, Julian; Rea, Mary C.; O'Sullivan, Orla; Ritari, Jarmo; Douillard, Francois P.
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. PUBLISHED peer-reviewed
Keyword(s): lactic-acid bacteria; crispr-cas systems; multiple sequence alignment; gram-positive bacteria; phylogenetic analysis; genus lactobacillus; molecular-cloning; protein; probiotics
Publication Date:
2015
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: University of Limerick
Funder(s): Science Foundation Ireland
Citation(s): Nature Communications;6: 8322
http://dx.doi.org/10.1038/ncomms9322
SFI/12/RC/2273
250172
R01DE019455
Publisher(s): Nature Publishing Group
First Indexed: 2016-04-16 05:25:32 Last Updated: 2018-07-12 06:35:37