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Nat Commun. 2015 Sep 29;6:8322. doi: 10.1038/ncomms9322.

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

Author information

1
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
2
School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
3
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
4
College of Dentistry, New York University, New York City, New York 10010, USA.
5
Department Life Sciences &MSSI, University of Limerick, V94 T9PX Limerick, Ireland.
6
Department of Biotechnology, University of Verona, Verona 37134, Italy.
7
Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland.
8
Wellcome Trust Sanger Centre, Hinxton, CB10 1SA, UK.
9
Department of Biotechnology, Teagasc, Moorepark, Fermoy Co. Cork P61 C996, Ireland.
10
Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA.
11
Laboratory of Microbiology, Wageningen University, Wageningen, 6703HB, The Netherlands.

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.

PMID:
26415554
PMCID:
PMC4667430
DOI:
10.1038/ncomms9322
[Indexed for MEDLINE]
Free PMC Article

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