Discovering lactic acid bacteria by genomics

Todd Klaenhammer; Eric Altermann; Fabrizio Arigoni; Alexander Bolotin; Fred Breidt; Jeffrey Broadbent; Raul Cano; Stephane Chaillou; Josef Deutscher; Mike Gasson; Maarten van de Guchte; Jean Guzzo; Axel Hartke; Trevor Hawkins; Pascal Hols; Robert Hutkins; Michiel Kleerebezem; Jan Kok; Oscar Kuipers; Mark Lubbers; Emmanuelle Maguin; Larry McKay; David Mills; Arjen Nauta; Ross Overbeek; Herman Pel; David Pridmore; Milton Saier; Douwe van Sinderen; Alexei Sorokin; James Steele; Daniel O'Sullivan; Willem de Vos; Bart Weimer; Monique Zagorec; Roland Siezen

doi:10.1023/A:1020638309912

Discovering lactic acid bacteria by genomics

Todd Klaenhammer, Eric Altermann, Fabrizio Arigoni, Alexander Bolotin, Fred Breidt, Jeffrey Broadbent, Raul Cano, Stephane Chaillou, Josef Deutscher, Mike Gasson, Maarten van de Guchte, Jean Guzzo, Axel Hartke, Trevor Hawkins, Pascal Hols, Robert Hutkins, Michiel Kleerebezem, Jan Kok, Oscar Kuipers, Mark LubbersEmmanuelle Maguin, Larry McKay, David Mills, Arjen Nauta, Ross Overbeek, Herman Pel, David Pridmore, Milton Saier, Douwe van Sinderen, Alexei Sorokin, James Steele, Daniel O'Sullivan, Willem de Vos, Bart Weimer, Monique Zagorec, Roland Siezen

Food Science and Nutrition

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

214 Scopus citations

Abstract

This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.

Original language	English (US)
Pages (from-to)	29-58
Number of pages	30
Journal	Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology
Volume	82
Issue number	1-4
DOIs	https://doi.org/10.1023/A:1020638309912
State	Published - Aug 2002

Bibliographical note

Funding Information:
This project was supported by Dairy Management, Inc, the Southeast Dairy Foods Research Center, the California Dairy Foods Research Center, the Environmental Biotechnology Institute and Rhodia, Inc. The efforts of Eric Altermann, Mike Russell, A. Hamrick, T. Cox, and D. Doherty are gratefully acknowledged.

Funding Information:
We acknowledge the participation of Yanick Auf-fray, Alain Mazé, Gregory Boël, Ivan Mijakovic, Jean-Christophe Giard, Jean Marie Laplace, Abdel-lah Benachour, Alain Rincé, Vianney Pichereau and the financial aide from the INRA, the Ministère de la Recherche and the Conseil Régionale de Basse-Normandie.

Funding Information:
We acknowledge the valuable contributes of Michael Collett, Christopher Pillidge, and Marie-Laure De-labre, and the financial support of our sponsors Vi-aLactia BioSciences NZ Ltd, the New Zealand Foundation for Research Science and Technology, and the Marsden Fund of the Royal Society of New Zealand.

Funding Information:
The Joint Genome Institute of the US Department of Energy and the Lactic Acid Bacteria Genome Consortium is supporting this sequencing project. The efforts of R. Barrangou, E. Altermann, W. M. Russell, T. Hawkins, S. Stilwagen, P. Richardson, and K. Kadner are gratefully acknowledged. Additional support was provided by Dairy Management, Inc, the Southeast Dairy Foods Research Center and Rhodia, Inc.

Funding Information:
This project was supported by the US Department of Energy–Joint Genome Institute, the American Vineyard Foundation, and the California Competitive Grants Program for Research in Viticulture and Enology. The efforts of C. M. Joseph, K. Ranstiou, T. Hawkins, S. Stilwagen, P. Richardson, and K. Kadner are gratefully acknowledged.

Funding Information:
This project was supported by Dairy Management, Inc. through the Wisconsin Center for Dairy Research and the Western Dairy Center, College of Agricultural and Life Sciences and Chr. Hansen, Inc. Fred Blattner and George F. Mayhew from the Genome Center of Wisconsin are thanked for their assistance with genome assembly and annotation.

Keywords

Bifidobacterium
Brevibacterium
Food
Genomics
Gram-positive bacteria
Health
Lactic acid bacteria
Lactobacillus
Lactococcus
Leuconostoc
Oenococcus
Pediococcus
Propionibacterium
Streptococcus

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10.1023/A:1020638309912

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Klaenhammer, T., Altermann, E., Arigoni, F., Bolotin, A., Breidt, F., Broadbent, J., Cano, R., Chaillou, S., Deutscher, J., Gasson, M., van de Guchte, M., Guzzo, J., Hartke, A., Hawkins, T., Hols, P., Hutkins, R., Kleerebezem, M., Kok, J., Kuipers, O., ... Siezen, R. (2002). Discovering lactic acid bacteria by genomics. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 82(1-4), 29-58. https://doi.org/10.1023/A:1020638309912

Klaenhammer, T, Altermann, E, Arigoni, F, Bolotin, A, Breidt, F, Broadbent, J, Cano, R, Chaillou, S, Deutscher, J, Gasson, M, van de Guchte, M, Guzzo, J, Hartke, A, Hawkins, T, Hols, P, Hutkins, R, Kleerebezem, M, Kok, J, Kuipers, O, Lubbers, M, Maguin, E, McKay, L, Mills, D, Nauta, A, Overbeek, R, Pel, H, Pridmore, D, Saier, M, van Sinderen, D, Sorokin, A, Steele, J, O'Sullivan, D, de Vos, W, Weimer, B, Zagorec, M & Siezen, R 2002, 'Discovering lactic acid bacteria by genomics', Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, vol. 82, no. 1-4, pp. 29-58. https://doi.org/10.1023/A:1020638309912

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abstract = "This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.",

keywords = "Bifidobacterium, Brevibacterium, Food, Genomics, Gram-positive bacteria, Health, Lactic acid bacteria, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Propionibacterium, Streptococcus",

author = "Todd Klaenhammer and Eric Altermann and Fabrizio Arigoni and Alexander Bolotin and Fred Breidt and Jeffrey Broadbent and Raul Cano and Stephane Chaillou and Josef Deutscher and Mike Gasson and {van de Guchte}, Maarten and Jean Guzzo and Axel Hartke and Trevor Hawkins and Pascal Hols and Robert Hutkins and Michiel Kleerebezem and Jan Kok and Oscar Kuipers and Mark Lubbers and Emmanuelle Maguin and Larry McKay and David Mills and Arjen Nauta and Ross Overbeek and Herman Pel and David Pridmore and Milton Saier and {van Sinderen}, Douwe and Alexei Sorokin and James Steele and Daniel O'Sullivan and {de Vos}, Willem and Bart Weimer and Monique Zagorec and Roland Siezen",

note = "Funding Information: This project was supported by Dairy Management, Inc, the Southeast Dairy Foods Research Center, the California Dairy Foods Research Center, the Environmental Biotechnology Institute and Rhodia, Inc. The efforts of Eric Altermann, Mike Russell, A. Hamrick, T. Cox, and D. Doherty are gratefully acknowledged. Funding Information: We acknowledge the participation of Yanick Auf-fray, Alain Maz{\'e}, Gregory Bo{\"e}l, Ivan Mijakovic, Jean-Christophe Giard, Jean Marie Laplace, Abdel-lah Benachour, Alain Rinc{\'e}, Vianney Pichereau and the financial aide from the INRA, the Minist{\`e}re de la Recherche and the Conseil R{\'e}gionale de Basse-Normandie. Funding Information: We acknowledge the valuable contributes of Michael Collett, Christopher Pillidge, and Marie-Laure De-labre, and the financial support of our sponsors Vi-aLactia BioSciences NZ Ltd, the New Zealand Foundation for Research Science and Technology, and the Marsden Fund of the Royal Society of New Zealand. Funding Information: The Joint Genome Institute of the US Department of Energy and the Lactic Acid Bacteria Genome Consortium is supporting this sequencing project. The efforts of R. Barrangou, E. Altermann, W. M. Russell, T. Hawkins, S. Stilwagen, P. Richardson, and K. Kadner are gratefully acknowledged. Additional support was provided by Dairy Management, Inc, the Southeast Dairy Foods Research Center and Rhodia, Inc. Funding Information: This project was supported by the US Department of Energy–Joint Genome Institute, the American Vineyard Foundation, and the California Competitive Grants Program for Research in Viticulture and Enology. The efforts of C. M. Joseph, K. Ranstiou, T. Hawkins, S. Stilwagen, P. Richardson, and K. Kadner are gratefully acknowledged. Funding Information: This project was supported by Dairy Management, Inc. through the Wisconsin Center for Dairy Research and the Western Dairy Center, College of Agricultural and Life Sciences and Chr. Hansen, Inc. Fred Blattner and George F. Mayhew from the Genome Center of Wisconsin are thanked for their assistance with genome assembly and annotation.",

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AU - Broadbent, Jeffrey

AU - Cano, Raul

AU - Chaillou, Stephane

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Discovering lactic acid bacteria by genomics

Abstract

Bibliographical note

Keywords

Access

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