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

• Published in: Nature communications Vol. 6; no. 1; p. 8322
• Main Authors: Sun, Zhihong, Harris, Hugh M. B., McCann, Angela, Guo, Chenyi, Argimón, Silvia, Zhang, Wenyi, Yang, Xianwei, Jeffery, Ian B, Cooney, Jakki C., Kagawa, Todd F., Liu, Wenjun, Song, Yuqin, Salvetti, Elisa, Wrobel, Agnieszka, Rasinkangas, Pia, Parkhill, Julian, Rea, Mary C., O’Sullivan, Orla, Ritari, Jarmo, Douillard, François P., Paul Ross, R., Yang, Ruifu, Briner, Alexandra E., Felis, Giovanna E., de Vos, Willem M., Barrangou, Rodolphe, Klaenhammer, Todd R., Caufield, Page W., Cui, Yujun, Zhang, Heping, O’Toole, Paul W.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29-09-2015; Nature Publishing Group; Nature Pub. Group
• Subjects: 631/1647/48; 631/326/325/2482; 631/61; Biotechnology; Genome, Bacterial; Humanities and Social Sciences; Laboratorium voor Microbiologie; Lactobacillus - enzymology; Lactobacillus - genetics; Leuconostoc - genetics; Microbiological Laboratory; Microbiologie; Microbiology; multidisciplinary; Pediococcus - genetics; Phylogeny; Science; Science (multidisciplinary); Sequence Analysis, DNA; VLAG
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms9322

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.
Lactobacillus
is a lactic acid bacteria and has a wide range of application from use in probiotic food production to biotherapeutics. Here, the authors sequence and compare the genomes of 213 different
Lactobacillus
strains and related genera, and provide new insight into phylogenomic organization and adaptive immunity elements in this bacteria family.