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. DouillardR. 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, Paul W. O'Toole

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number8322
JournalNature Communications
Volume6
DOIs
StatePublished - Sep 29 2015

Fingerprint

biotechnology
genome
Lactobacillus
Biotechnology
Genomics
food
Bacteriocin Plasmids
Clustered Regularly Interspaced Short Palindromic Repeats
Food preservation
Genes
immune systems
editing
lactic acid
Immune system
Biodiversity
carbohydrates
nutrients
classifying
bacteria
Nutrients

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

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

In: Nature Communications, Vol. 6, 8322, 29.09.2015.

Research output: Contribution to journalArticle

Sun, Z, Harris, HMB, McCann, A, Guo, C, Argimón, S, Zhang, W, Yang, X, Jeffery, IB, Cooney, JC, Kagawa, TF, Liu, W, Song, Y, Salvetti, E, Wrobel, A, Rasinkangas, P, Parkhill, J, Rea, MC, O'Sullivan, O, Ritari, J, Douillard, FP, Paul Ross, R, Yang, R, Briner, AE, Felis, GE, De Vos, WM, Barrangou, R, Klaenhammer, TR, Caufield, PW, Cui, Y, Zhang, H & O'Toole, PW 2015, 'Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera', Nature Communications, vol. 6, 8322. https://doi.org/10.1038/ncomms9322
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. / Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. In: Nature Communications. 2015 ; Vol. 6.
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AU - Argimón, Silvia

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AU - Briner, Alexandra E.

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AU - Barrangou, Rodolphe

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