Comparative genomics of Lactobacillus and other LAB

Trudy M. Wassenaar, Oksana Lukjancenko

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    Abstract

    The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species, twelve Enterococcus genomes of four species and a single Weissella genome. Genomes of pathogenic strains or species were not included. Since the gene density in these genomes is relatively constant, genome size is a measure of gene content. The genomes of Enterococcus were significantly larger than that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively high for Lb. sanfransiscensis and Lb. salivarius, with respect to their moderate gene size. The phylogenetic relationship of the 16S ribosomal RNA genes of these genomes was established and pan- and core genomes were defined for each genus. In addition, core genome analysis was performed on all food isolates combined, as well as for all isolates that had been obtained from the gastro-intestinal tract of animals or humans. The Clusters of Orthologous Genes were deduced and compared for these core genomes. The presented data aim to illustrate how genome comparisons can complement experimental observations.
    Original languageEnglish
    Title of host publicationLactic Acid Bacteria : Biodiversity and Taxonomy
    EditorsWilhelm H. Holzapfel, Brian J.B. Wood
    Number of pages15
    Place of PublicationUnited Kingdom
    PublisherWiley-Blackwell
    Publication date2014
    Pages55-69
    Chapter5
    ISBN (Print)9781444333831
    ISBN (Electronic)9781118655252
    DOIs
    Publication statusPublished - 2014

    Keywords

    • Core genome
    • Genome comparison
    • Lactococcus
    • Leuconostoc
    • Pan-genome
    • Probiotics

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