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

被引：428

作者：

Sun, Zhihong ^{[1
]}

Harris, Hugh M. B. ^{[2
]}

McCann, Angela ^{[2
]}

Guo, Chenyi ^{[3
]}

Argimon, Silvia ^{[4
]}

Zhang, Wenyi ^{[1
]}

Yang, Xianwei ^{[3
]}

Jeffery, Ian B. ^{[2
]}

Cooney, Jakki C. ^{[5
]}

Kagawa, Todd F. ^{[5
]}

Liu, Wenjun ^{[1
]}

Song, Yuqin ^{[1
]}

Salvetti, Elisa ^{[6
]}

Wrobel, Agnieszka ^{[2
]}

Rasinkangas, Pia ^{[7
]}

Parkhill, Julian ^{[8
]}

Rea, Mary C. ^{[9
]}

O'Sullivan, Orla ^{[9
]}

Ritari, Jarmo ^{[7
]}

Douillard, Francois P. ^{[7
]}

Ross, R. Paul ^{[9
]}

Yang, Ruifu ^{[3
]}

Briner, Alexandra E. ^{[10
]}

Felis, Giovanna E. ^{[6
]}

de Vos, Willem M. ^{[7
,11
]}

Barrangou, Rodolphe ^{[10
]}

Klaenhammer, Todd R. ^{[10
]}

Caufield, Page W. ^{[4
]}

Cui, Yujun ^{[3
]}

Zhang, Heping ^{[1
]}

O'Toole, Paul W. ^{[2
]}

机构：

[1] Inner Mongolia Agr Univ, Educ Minist China, Key Lab Dairy Biotechnol & Engn, Hohhot 010018, Inner Mongolia, Peoples R China

[2] Natl Univ Ireland Univ Coll Cork, Sch Microbiol, Alimentary Pharmabiot Ctr, Cork T12 Y337, Ireland

[3] Beijing Inst Microbiol & Epidemiol, State Key Lab Pathogen & Biosecur, Beijing 100071, Peoples R China

[4] NYU, Coll Dent, New York, NY 10010 USA

[5] Univ Limerick, Dept Life Sci & MSSI, Limerick V94 T9PX, Ireland

[6] Univ Verona, Dept Biotechnol, I-37134 Verona, Italy

[7] Univ Helsinki, Dept Vet Biosci, Helsinki 00014, Finland

[8] Wellcome Trust Sanger Ctr, Hinxton CB10 1SA, England

[9] TEAGASC, Dept Biotechnol, Fermoy P61 C996, Cork, Ireland

[10] N Carolina State Univ, Dept Food Bioproc & Nutr Sci, Raleigh, NC 27695 USA

[11] Wageningen Univ, Microbiol Lab, NL-6703 HB Wageningen, Netherlands

来源：

NATURE COMMUNICATIONS | 2015年 / 6卷

基金：

中国国家自然科学基金; 欧洲研究理事会; 爱尔兰科学基金会; 芬兰科学院;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; GLYCOSIDE HYDROLASE FAMILY; LACTIC-ACID BACTERIA; PHYLOGENETIC ANALYSIS; GENUS LACTOBACILLUS; MOLECULAR-CLONING; PROBIOTICS; DNA; RECONSTRUCTION; METABOLISM;

D O I：

10.1038/ncomms9322

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：13

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