title: The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content.
abstract: 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.
authors.affiliation: Center for Molecular and Biomolecular Informatics, 6525ED, Nijmegen, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Boekhorst
authors.affiliation: NIZO food research, 6710 BA Ede, The Netherlands.|Wageningen Centre for Food Sciences, 6700 AN Wageningen, The Netherlands.|Center for Molecular and Biomolecular Informatics, 6525ED, Nijmegen, The Netherlands.
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: Marie-Camille
authors.initials: MC
authors.lastname: Zwahlen
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Vilanova
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: Raymond D
authors.initials: RD
authors.lastname: Pridmore
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: Annick
authors.initials: A
authors.lastname: Mercenier
authors.affiliation: NIZO food research, 6710 BA Ede, The Netherlands.|Wageningen Centre for Food Sciences, 6700 AN Wageningen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
authors.affiliation: Wageningen Centre for Food Sciences, 6700 AN Wageningen, The Netherlands.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: Harald
authors.initials: H
authors.lastname: Brüssow
authors.affiliation: Nestlé Research Center, Nestec SA, 1000 Lausanne 26, Switzerland.
authors.forename: Frank
authors.initials: F
authors.lastname: Desiere
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000235:genetics; D001692:Biological Transport / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics*; D003067:Coenzymes / Q000235:genetics; D004251:DNA Transposable Elements; D003673:Defective Viruses / Q000235:genetics; D004798:Enzymes / Q000235:genetics; D005227:Fatty Acids / Q000096:biosynthesis; D023061:Gene Order; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007778:Lactobacillus / Q000235:genetics*; D048191:Lactiplantibacillus plantarum / Q000235:genetics; D005810:Multigene Family; D009711:Nucleotides / Q000096:biosynthesis; D039002:Prophages; D012329:RNA, Bacterial / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D011995:Recombination, Genetic; D017386:Sequence Homology, Amino Acid; D012407:rRNA Operon
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D003067:Coenzymes; D004251:DNA Transposable Elements; D004798:Enzymes; D005227:Fatty Acids; D009711:Nucleotides; D012329:RNA, Bacterial; D012343:RNA, Transfer