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Title: Comparative genomics of the lactic acid bacteria

Abstract

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1165212
Report Number(s):
LBNL-6788E
Journal ID: ISSN 0027--8424
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
PNAS
Additional Journal Information:
Journal Volume: 103; Journal Issue: 42; Related Information: Journal Publication Date: October 17, 2006; Journal ID: ISSN 0027--8424
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; evolutionary genomics, fermentation

Citation Formats

Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J. -H., Diaz-Muniz, I., Dosti, B., Smeianov, V, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., and Mills, D. Comparative genomics of the lactic acid bacteria. United States: N. p., 2006. Web. doi:10.1073/pnas.0607117103.
Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J. -H., Diaz-Muniz, I., Dosti, B., Smeianov, V, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., & Mills, D. Comparative genomics of the lactic acid bacteria. United States. https://doi.org/10.1073/pnas.0607117103
Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J. -H., Diaz-Muniz, I., Dosti, B., Smeianov, V, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., and Mills, D. 2006. "Comparative genomics of the lactic acid bacteria". United States. https://doi.org/10.1073/pnas.0607117103. https://www.osti.gov/servlets/purl/1165212.
@article{osti_1165212,
title = {Comparative genomics of the lactic acid bacteria},
author = {Makarova, K. and Slesarev, A. and Wolf, Y. and Sorokin, A. and Mirkin, B. and Koonin, E. and Pavlov, A. and Pavlova, N. and Karamychev, V. and Polouchine, N. and Shakhova, V. and Grigoriev, I. and Lou, Y. and Rokhsar, D. and Lucas, S. and Huang, K. and Goodstein, D. M. and Hawkins, T. and Plengvidhya, V. and Welker, D. and Hughes, J. and Goh, Y. and Benson, A. and Baldwin, K. and Lee, J. -H. and Diaz-Muniz, I. and Dosti, B. and Smeianov, V and Wechter, W. and Barabote, R. and Lorca, G. and Altermann, E. and Barrangou, R. and Ganesan, B. and Xie, Y. and Rawsthorne, H. and Tamir, D. and Parker, C. and Breidt, F. and Broadbent, J. and Hutkins, R. and O'Sullivan, D. and Steele, J. and Unlu, G. and Saier, M. and Klaenhammer, T. and Richardson, P. and Kozyavkin, S. and Weimer, B. and Mills, D.},
abstractNote = {Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.},
doi = {10.1073/pnas.0607117103},
url = {https://www.osti.gov/biblio/1165212}, journal = {PNAS},
issn = {0027--8424},
number = 42,
volume = 103,
place = {United States},
year = {Thu Jun 01 00:00:00 EDT 2006},
month = {Thu Jun 01 00:00:00 EDT 2006}
}