title: Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.
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.
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Sun
authors.affiliation: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
authors.forename: Hugh M B
authors.initials: HM
authors.lastname: Harris
authors.affiliation: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
authors.forename: Angela
authors.initials: A
authors.lastname: McCann
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Chenyi
authors.initials: C
authors.lastname: Guo
authors.affiliation: College of Dentistry, New York University, New York City, New York 10010, USA.
authors.forename: Silvia
authors.initials: S
authors.lastname: Argimón
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
authors.forename: Wenyi
authors.initials: W
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.affiliation: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
authors.forename: Ian B
authors.initials: IB
authors.lastname: Jeffery
authors.affiliation: Department Life Sciences &MSSI, University of Limerick, V94 T9PX Limerick, Ireland.
authors.forename: Jakki C
authors.initials: JC
authors.lastname: Cooney
authors.affiliation: Department Life Sciences &MSSI, University of Limerick, V94 T9PX Limerick, Ireland.
authors.forename: Todd F
authors.initials: TF
authors.lastname: Kagawa
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Liu
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Song
authors.affiliation: Department of Biotechnology, University of Verona, Verona 37134, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Salvetti
authors.affiliation: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Wrobel
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Pia
authors.initials: P
authors.lastname: Rasinkangas
authors.affiliation: Wellcome Trust Sanger Centre, Hinxton, CB10 1SA, UK.
authors.forename: Julian
authors.identifier: http://orcid.org/0000-0002-7069-5958
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Department of Biotechnology, Teagasc, Moorepark, Fermoy Co. Cork P61 C996, Ireland.
authors.forename: Mary C
authors.initials: MC
authors.lastname: Rea
authors.affiliation: Department of Biotechnology, Teagasc, Moorepark, Fermoy Co. Cork P61 C996, Ireland.
authors.forename: Orla
authors.initials: O
authors.lastname: O'Sullivan
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Jarmo
authors.initials: J
authors.lastname: Ritari
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland.
authors.forename: François P
authors.initials: FP
authors.lastname: Douillard
authors.affiliation: Department of Biotechnology, Teagasc, Moorepark, Fermoy Co. Cork P61 C996, Ireland.
authors.forename: R
authors.initials: R
authors.lastname: Paul Ross
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA.
authors.forename: Alexandra E
authors.initials: AE
authors.lastname: Briner
authors.affiliation: Department of Biotechnology, University of Verona, Verona 37134, Italy.
authors.forename: Giovanna E
authors.initials: GE
authors.lastname: Felis
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland.|Laboratory of Microbiology, Wageningen University, Wageningen, 6703HB, The Netherlands.
authors.forename: Willem M
authors.identifier: http://orcid.org/0000-0002-0273-3166
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA.
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA.
authors.forename: Todd R
authors.initials: TR
authors.lastname: Klaenhammer
authors.affiliation: College of Dentistry, New York University, New York City, New York 10010, USA.
authors.forename: Page W
authors.initials: PW
authors.lastname: Caufield
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
authors.forename: Heping
authors.initials: H
authors.lastname: Zhang
authors.affiliation: School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
authors.forename: Paul W
authors.initials: PW
authors.lastname: O'Toole
mesh_terms: D001709:Biotechnology; D016680:Genome, Bacterial; D007778:Lactobacillus / Q000201:enzymology / Q000235:genetics*; D007934:Leuconostoc / Q000235:genetics; D010376:Pediococcus / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA