Page Banner

United States Department of Agriculture

Agricultural Research Service

Title: Comparative genomics of the lactic acid bacteria

Authors
item Makarova, K - NAT. INST. OF HEALTH
item Slesarev, A - FIDELITY SYSTEMS
item Wolf, Y - NAT. INST. OF HEALTH
item Sorokin, A - NAT. INST. OF HEALTH
item Mirkin, B - UNIV. OF LONDON
item Koonin, E - NAT. INST. OF HEALTH
item Pavlov, A - FIDELITY SYSTEMS
item Pavlova, N - FIDELITY SYSTEMS
item Karamychev, V - FIDELITY SYSTEMS
item Polouchine, N - FIDELITY SYSTEMS
item Shakhova, V - FIDELITY SYSTEMS
item Grigoriev, I - USDOE JGI
item Lou, Y - USDOE JGI
item Rohksar, D - USDOE JGI
item Lucas, S - USDOE JGI
item Huang, K - USDOE JGI
item Goodstein, D - USDOE JGI
item Hawkins, T - USDOE JGI
item Plengvidhya, V - NC STATE UNIV
item Welker, D - UTAH STATE UNIV
item Hughes, J - UTAH STATE UNIV
item Goh, Y - UNIV OF NEBRASKA
item Benson, A - UNIV OF NEBRASKA
item Baldwin, K - UNIV OF MINNESOTA
item Lee, J - UNIV OF MINNESOTA
item Perez Diaz, Ilenys
item Dosti, B - UNIV OF WISCONSIN
item Smeianov, V - UNIV OF WISCONSIN
item Wechter, William
item Barabote, R - UNIV OF CALIFORNIA
item Lorca, G - UNIV OF CALIFORNIA
item Altermann, E - NC STATE UNIV
item Barrangou, R - NC STATE UNIV
item Ganesan, B - UTAH STATE UNIV
item Xie, Y - UTAH STATE UNIV
item Rawsthorne, H - UNIV OF CALIFORNIA
item Tamir, D - UNIV OF CALIFORNIA
item Parker, C - UNIV OF CALIFORNIA
item Breidt, Frederick
item Broadbent, J - UNIV OF IDAHO
item Hutkins, R - UNIV OF NEBRASKA
item O'Sullivan, D - UNIV OF MINNESOTA
item Steele, J - UNIV OF WISCONSIN
item Unlu, G - UNIV OF IDAHO
item Saier, M - UNIV OF CALIFORNIA
item Klaenhammer, T - NC STATE UNIV
item Richardson, P - USDOE JGI
item Kozyavkin, S - FIDELITY SYSTEMS
item Weimer, B - UTAH STATE UNIV
item Mills, D - UNIV OF CALIFORNIA

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 21, 2006
Publication Date: October 17, 2006
Repository URL: http://hdl.handle.net/10113/2385
Citation: 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., Rohksar, 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., Perez Diaz, I.M., Dosti, B., Smeianov, V., Wechter, W.P., 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. 2006. Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences. 103(42):15611-15616.

Interpretive Summary: This manuscript contains a report of the complete sequencing of the chromosomal DNA from nine lactic bacteria. These bacteria are all important in industrial food fermentations. Currently only six complete lactic acid bacterial genome sequences are known, so this manuscript represents a significant leap forward in the understanding of genetics (genomics) of this important group of bacteria. A comparative analysis of the sequence results for the nine bacteria is presented. The results give important clues to how this group of bacteria evolved, as well as the potential for biochemical reactions encoded the DNA. The DNA sequences will be submitted to public databases with the publication of this manuscript, allowing researchers around the world to have access to this valuable resource. The results of studies based on these data will very likely lead to significant advances in our understanding food fermentations.

Technical 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 pathways. 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 co-evolution of lactic acid bacteria with their habitats.

Last Modified: 10/21/2014