Comparative genomics of the lactic acid bacteria

Kira S. Makarova1, Alexeï Slesarev2, Yuri I. Wolf1, Alexeï Sorokin1, Boris Mirkin3, Eugene V. Koonin1, А. В. Павлов2, Nadejda V. Pavlova2, Valeri N. Karamychev2, Nikolai Polouchine2, Vera V. Shakhova2, Igor V. Grigoriev4, Yunian Lou4, Daniel S. Rohksar4, Susan Lucas4, Kunlun Huang4, David Goodstein4, Trevor Hawkins4, Vethachai Plengvidhya5,6, Dennis L. Welker7, Judith M. Hughes7, Yong Jun Goh8, Andrew K. Benson8, Kathleen A. Baldwin9, Jung Lee9, I. Díaz-Muñiz10, Bilal Dosti10, Smeianov Vv10, W. Patrick Wechter10, Ravi D. Barabote11, Graciela L. Lorca11, Eric Altermann12, Rodolphe Barrangou12, Balasubramanian Ganesan13, Yi Xie13,14, Helen Rawsthorne15, Dafna Tamir15,16, Christina Pierpaoli Parker15,16, Fred Breidt5,6, Jeffery R. Broadbent17, Robert W. Hutkins8, Daniel J. O’Sullivan9, J. L. Steele10, Gülhan Ünlü18, Milton H. Saier11, Todd R. Klaenhammer12, Daniel S. Rokhsar4, Sergei A. Kozyavkin2, Bart C. Weimer13,14, David A. Mills15
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;
2Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879;
3School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom;
4U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598;
5Department of Food Science, North Carolina State University, Raleigh, NC 27695;; North Carolina Agricultural Research Service, U.S. Department of Agriculture, Raleigh, NC 27695; Departments of
6North Carolina Agricultural Research Service, U.S. Department of Agriculture, Raleigh, NC 27695; Departments of
7Biology and
8Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583
9Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, 55108
10Department of Food Science, University of Wisconsin, Madison, WI 53706
11Department of Biology, University of California at San Diego, La Jolla, CA 92093
12Department of Food Science, North Carolina State University, Raleigh, NC 27695;
13Center for Integrated BioSystems, Utah State University, Logan, UT 84322;
14Center for Integrated BioSystems, Utah State University, Logan, UT 84322;; Nutrition and Food Science and
15Department of Viticulture and Enology, University of California, Davis, CA 95616; and
16Department of Viticulture and Enology, University of California, Davis, CA 95616; and; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;
17Nutrition and Food Science and
18Department of Food Science and Toxicology, University of Idaho, Moscow, ID 83844

Tóm tắt

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.

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