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; Paul W. O'Toole

doi:10.1038/ncomms9322

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

Cariology and Comprehensive Care

Research output: Contribution to journal › Article › peer-review

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 language	English (US)
Article number	8322
Journal	Nature communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms9322
State	Published - Sep 29 2015

ASJC Scopus subject areas

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

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Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., Liu, W., Song, Y., Salvetti, E., Wrobel, A., Rasinkangas, P., Parkhill, J., Rea, M. C., O'Sullivan, O., Ritari, J., ... O'Toole, P. W. (2015). Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nature communications, 6, [8322]. https://doi.org/10.1038/ncomms9322

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 journal › Article › peer-review

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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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.",

author = "Zhihong Sun and Harris, {Hugh M.B.} and Angela McCann and Chenyi Guo and Silvia Argim{\'o}n and Wenyi Zhang and Xianwei Yang and Jeffery, {Ian B.} and Cooney, {Jakki C.} and Kagawa, {Todd F.} and Wenjun Liu and Yuqin Song and Elisa Salvetti and Agnieszka Wrobel and Pia Rasinkangas and Julian Parkhill and Rea, {Mary C.} and Orla O'Sullivan and Jarmo Ritari and Douillard, {Fran{\c c}ois P.} and {Paul Ross}, R. and Ruifu Yang and Briner, {Alexandra E.} and Felis, {Giovanna E.} and {De Vos}, {Willem M.} and Rodolphe Barrangou and Klaenhammer, {Todd R.} and Caufield, {Page W.} and Yujun Cui and Heping Zhang and O'Toole, {Paul W.}",

note = "Funding Information: Work in laboratories of P.W.O{\textquoteright}T. and P.W.C. was supported by an R01 award from the US National Institute of Dental and Craniofacial Research (R01DE019455). P.W.O{\textquoteright}T. was also supported by Science Foundation Ireland through Principal Investigator Award 07-IN.1-B1780, and by a Centre award to the Alimentary Pharmabiotic Centre (grant number SFI/12/RC/2273). Work in Huhhot was supported by the National Natural Science Foundation of China (grant code 31430066), and in Beijing by the State Key Development Program for Basic Research of China (grant code 2015CB554202). Work in Helsinki was supported by the Academy of Finland (Grants 141140 and 252123 to W.M.deV. and F.P.D.) and the European Research Council (Advanced Grant 250172 to W.M.deV.). We also acknowledge Dr Fabien Cousin for his useful advice on the most up-to-date Lactobacillus species reclassifications. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited. All rights reserved.",

year = "2015",

month = sep,

day = "29",

doi = "10.1038/ncomms9322",

language = "English (US)",

volume = "6",

journal = "Nature Communications",

issn = "2041-1723",

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T1 - Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

AU - Sun, Zhihong

AU - Harris, Hugh M.B.

AU - McCann, Angela

AU - Guo, Chenyi

AU - Argimón, Silvia

AU - Zhang, Wenyi

AU - Yang, Xianwei

AU - Jeffery, Ian B.

AU - Cooney, Jakki C.

AU - Kagawa, Todd F.

AU - Liu, Wenjun

AU - Song, Yuqin

AU - Salvetti, Elisa

AU - Wrobel, Agnieszka

AU - Rasinkangas, Pia

AU - Parkhill, Julian

AU - Rea, Mary C.

AU - O'Sullivan, Orla

AU - Ritari, Jarmo

AU - Douillard, François P.

AU - Paul Ross, R.

AU - Yang, Ruifu

AU - Briner, Alexandra E.

AU - Felis, Giovanna E.

AU - De Vos, Willem M.

AU - Barrangou, Rodolphe

AU - Klaenhammer, Todd R.

AU - Caufield, Page W.

AU - Cui, Yujun

AU - Zhang, Heping

AU - O'Toole, Paul W.

N1 - Funding Information: Work in laboratories of P.W.O’T. and P.W.C. was supported by an R01 award from the US National Institute of Dental and Craniofacial Research (R01DE019455). P.W.O’T. was also supported by Science Foundation Ireland through Principal Investigator Award 07-IN.1-B1780, and by a Centre award to the Alimentary Pharmabiotic Centre (grant number SFI/12/RC/2273). Work in Huhhot was supported by the National Natural Science Foundation of China (grant code 31430066), and in Beijing by the State Key Development Program for Basic Research of China (grant code 2015CB554202). Work in Helsinki was supported by the Academy of Finland (Grants 141140 and 252123 to W.M.deV. and F.P.D.) and the European Research Council (Advanced Grant 250172 to W.M.deV.). We also acknowledge Dr Fabien Cousin for his useful advice on the most up-to-date Lactobacillus species reclassifications. Publisher Copyright: © 2015 Macmillan Publishers Limited. All rights reserved.

PY - 2015/9/29

Y1 - 2015/9/29

N2 - 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.

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

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