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

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. Douillard, 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 () and Paul W. O’Toole ()
Additional contact information
Zhihong Sun: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University
Hugh M. B. Harris: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork
Angela McCann: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork
Chenyi Guo: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
Silvia Argimón: College of Dentistry, New York University
Wenyi Zhang: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University
Xianwei Yang: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
Ian B Jeffery: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork
Jakki C. Cooney: University of Limerick
Todd F. Kagawa: University of Limerick
Wenjun Liu: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University
Yuqin Song: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University
Elisa Salvetti: University of Verona
Agnieszka Wrobel: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork
Pia Rasinkangas: University of Helsinki
Julian Parkhill: Wellcome Trust Sanger Centre
Mary C. Rea: Department of Biotechnology
Orla O’Sullivan: Department of Biotechnology
Jarmo Ritari: University of Helsinki
François P. Douillard: University of Helsinki
R. Paul Ross: Department of Biotechnology
Ruifu Yang: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
Alexandra E. Briner: Bioprocessing and Nutrition Sciences, North Carolina State University
Giovanna E. Felis: University of Verona
Willem M. de Vos: University of Helsinki
Rodolphe Barrangou: Bioprocessing and Nutrition Sciences, North Carolina State University
Todd R. Klaenhammer: Bioprocessing and Nutrition Sciences, North Carolina State University
Page W. Caufield: College of Dentistry, New York University
Yujun Cui: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
Heping Zhang: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University
Paul W. O’Toole: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork

Nature Communications, 2015, vol. 6, issue 1, 1-13

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.

Date: 2015
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DOI: 10.1038/ncomms9322

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