Comparative genomics of the lactic acid bacteria - PubMed (original) (raw)

. 2006 Oct 17;103(42):15611-6.

doi: 10.1073/pnas.0607117103. Epub 2006 Oct 9.

A Slesarev, Y Wolf, A Sorokin, B Mirkin, E Koonin, A Pavlov, N Pavlova, V Karamychev, N Polouchine, V Shakhova, I Grigoriev, Y Lou, D Rohksar, S Lucas, K Huang, D M Goodstein, T Hawkins, V Plengvidhya, D Welker, J Hughes, Y Goh, A Benson, K Baldwin, J-H Lee, I Díaz-Muñiz, B Dosti, V Smeianov, W Wechter, R Barabote, G Lorca, E Altermann, R Barrangou, B Ganesan, Y Xie, H Rawsthorne, D Tamir, C Parker, F Breidt, J Broadbent, R Hutkins, D O'Sullivan, J Steele, G Unlu, M Saier, T Klaenhammer, P Richardson, S Kozyavkin, B Weimer, D Mills

Affiliations

Comparative genomics of the lactic acid bacteria

K Makarova et al. Proc Natl Acad Sci U S A. 2006.

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Phylogenetic trees of Lactobacillales constructed on the basis of concatenated alignments of ribosomal proteins. All branches are supported at >75% bootstrap values. Species are colored according to the current taxonomy: Lactobacillaceae, blue; Leuconostocaceae, magenta; Streptococcaceae, red.

Fig. 2.

Fig. 2.

Conserved and unique genes in the genomes of Lactobacillales. “Homolog” indicates genes with detectable homologs in organisms other than those analyzed here but could not be included in any of the COG sets. “Orphans” are predicted genes without detectable homologs. Lacga, Lb. gasseri; Lacbr, Lb. brevis; Pedpe, P. pentosaceus; Laccr, Lc. lactis ssp. cremoris; Strth, S. thermophilus; Oenoe, O. oeni; Leume, Le. mesenteroides; Lacca, Lb. casei; Lacde, Lb. delbrueckii; Lacla, Lc. lactis; Lacpl, Lb. plantarum; Lacjo, Lb. johnsonii. The vertical axis shows the number of genes per genome.

Fig. 3.

Fig. 3.

Reconstruction of gene content evolution in Lactobacillales. The tree topology is as in Fig. 1, rooted by using Baccillus subtilis as the outgroup. For each species and each internal node of tree, the inferred number of LaCOGs present, and the numbers of LaCOGs lost (blue) and gained (red) along the branch leading to the given node (species) are indicated. Abbreviations are as in Fig. 2.

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References

    1. Miller N, Wetterstrom W. In: The Cambridge World History of Food. Kiple K, Ornelas K, editors. Vol 2. Cambridge, UK: Cambridge Univ Press; 2000. pp. 1123–1139.
    1. Wood B. Microbiology of Fermented Foods. London: Blackie; 1998.
    1. Kandler O. Antonie van Leeuwenhoek. 1983;49:209–224. - PubMed
    1. Altermann E, Russell W, Azcarate-Peril M, Barrangou R, Buck B, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, et al. Proc Natl Acad Sci USA. 2005;102:3906–3912. - PMC - PubMed
    1. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich S, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch G, et al. Nat Biotechnol. 2004;22:1554–1558. - PMC - PubMed

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