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The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content

¹ Center for Molecular and Biomolecular Informatics, 6525ED, Nijmegen, The Netherlands
² Wageningen Centre for Food Sciences, 6700 AN Wageningen, The Netherlands
³ Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland
⁴ NIZO food research, 6710 BA Ede, The Netherlands

Correspondence
Jos Boekhorst
J.Boekhorst{at}cmbi.kun.nl

The first comprehensive comparative analysis of lactobacilli was done by comparing the genomes of Lactobacillus plantarum (3·3 Mb) and Lactobacillus johnsonii (2·0 Mb). L. johnsonii is predominantly found in the gastrointestinal tract, while L. plantarum is also found on plants and plant-derived material, and is used in a variety of industrial fermentations. The L. plantarum and L. johnsonii chromosomes have only 28 regions with conservation of gene order, totalling about 0·75 Mb; these regions are not co-linear, indicating major chromosomal rearrangements. Metabolic reconstruction indicates many differences between L. johnsonii and L. plantarum: numerous enzymes involved in sugar metabolism and in biosynthesis of amino acids, nucleotides, fatty acids and cofactors are lacking in L. johnsonii. Major differences were seen in the number and types of putative extracellular proteins, which are of interest because of their possible role in host–microbe interactions. The differences between L. plantarum and L. johnsonii, both in genome organization and gene content, are exceptionally large for two bacteria of the same genus, emphasizing the difficulty in taxonomic classification of lactobacilli.

Details of the size and location of conserved gene clusters in L. plantarum and L. johnsonii may be found in Supplementary Table S1; the number of proteins of L. plantarum and L. johnsonii for all COG classes in Supplementary Table S2; a KEGG comparison of major differences between L. plantarum and L. johnsonii in Supplementary Table S3; L. johnsonii and L. plantarum API 50 test results in Supplementary Table S4; the redundancy of enzymes involved in pyruvate metabolism in Supplementary Table S5; gene clusters encoding functionally related proteins present in L. plantarum but not in L. johnsonii and vice versa in Supplementary Table S6; lists of proteins unique to either L. plantarum or L. johnsonii in Supplementary Tables S7–S12; lists of proteins involved in the biosynthesis of polysaccharides, bacteriocins and prophages in Supplementary Table S13 with the online version of this paper at http://mic.sgmjournals.org.

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