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Published online on October 9, 2006, 10.1073/pnas.0607117103

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*Gene*Genome
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*LACTIC ACID
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Microbiology
Comparative genomics of the lactic acid bacteria

( evolutionary genomics | fermentation )

K. Makarova a, A. Slesarev b, Y. Wolf a, A. Sorokin a, B. Mirkin c, E. Koonin a,d, A. Pavlov b, N. Pavlova b, V. Karamychev b, N. Polouchine b, V. Shakhova b, I. Grigoriev e, Y. Lou e, D. Rohksar e, S. Lucas e, K. Huang e,f, D. M. Goodstein e, T. Hawkins e,f, V. Plengvidhya f,g,h, D. Welker i, J. Hughes i, Y. Goh j, A. Benson j, K. Baldwin k, J.-H. Lee k, I. Díaz-Muñiz f,l, B. Dosti l, V. Smeianov l, W. Wechter f,l, R. Barabote m, G. Lorca f,m, E. Altermann f,g, R. Barrangou f,g, B. Ganesan n,o, Y. Xie f,n,o, H. Rawsthorne f,p, D. Tamir f,p, C. Parker f,p, F. Breidt g,h, J. Broadbent o, R. Hutkins j, D. O'Sullivan k, J. Steele l, G. Unlu q, M. Saier m, T. Klaenhammer d,g, P. Richardson e, S. Kozyavkin b, B. Weimer d,n,o, and D. Mills d,p

aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; bFidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879; cSchool of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom; eU.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598; gDepartment of Food Science, North Carolina State University, Raleigh, NC 27695; hNorth Carolina Agricultural Research Service, U.S. Department of Agriculture, Raleigh, NC 27695; Departments of iBiology and oNutrition and Food Science and nCenter for Integrated BioSystems, Utah State University, Logan, UT 84322; jDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE 68583; kDepartment of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108; lDepartment of Food Science, University of Wisconsin, Madison, WI 53706; mDepartment of Biology, University of California at San Diego, La Jolla, CA 92093; pDepartment of Viticulture and Enology, University of California, Davis, CA 95616; and qDepartment of Food Science and Toxicology, University of Idaho, Moscow, ID 83844

Contributed by T. Klaenhammer, August 16, 2006

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.

Author contributions: A. Slesarev, E.K., T.H., F.B., J.B., R.H., D.O., J.S., G.U., M.S., T.K., P.R., S.K., B.W., and D.M. designed research; K.M., A. Slesarev, A. Sorokin, B.M., A.P., N. Pavlova, V.K., N. Polouchine, V. Shakhova, I.G., Y.L., S.L., K.H., D.M.G., V.P., D.W., J.H., Y.G., K.B., J.-H.L., I.D.-M., B.D., V. Smeianov, W.W., R. Barabote, G.L., E.A., R. Barrangou, B.G., Y.X., H.R., D.T., C.P., and S.K. performed research; A.P., N. Pavlova, N. Polouchine, B.G., Y.X., and S.K. contributed new reagents/analytic tools; A. Slesarev, Y.W., A.P., V.K., I.G., D.R., A.B., G.L., E.A., R. Barrangou, F.B., J.B., R.H., D.O., J.S., G.U., M.S., T.K., P.R., S.K., B.W., and D.M. analyzed data; and K.M., Y.W., E.K., T.K., P.R., S.K., and D.M. wrote the paper.

The authors declare no conflict of interest.

dTo whom correspondence may be addressed.

fPresent addresses for K.H., T.H., V.P., I.D.-M., W.W., G.L., E.A., R. Barrangou, Y.X., H.R., D.T., and C.P. are published as supporting information on the PNAS web site.

E. Koonin, E-mail: koonin{at}ncbi.,nlm.nih.gov
T. Klaenhammer, E-mail: trk{at}unity.ncsu.edu
B. Weimer, E-mail: bcweimer{at}cc.usu.edu
D. Mills, E-mail: damills{at}ucdavis.edu

www.pnas.org/cgi/doi/10.1073/pnas.0607117103
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