title: Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.
abstract: The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species.
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.
authors.forename: Maria Elena
authors.initials: ME
authors.lastname: Martino
authors.affiliation: Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud UMC, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
authors.forename: Jumamurat R
authors.initials: JR
authors.lastname: Bayjanov
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, 14195, Germany.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Caffrey
authors.affiliation: NIZO food research, P.O. Box 20, 6710 BA, Ede, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Joncour
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Hughes
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Gillet
authors.affiliation: Host Microbe Interactomics Group, Wageningen University, De Elst 1, 6708WD, Wageningen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
authors.affiliation: Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud UMC, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.|NIZO food research, P.O. Box 20, 6710 BA, Ede, The Netherlands.
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.
authors.forename: François
authors.initials: F
authors.lastname: Leulier
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D004777:Environment; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D048191:Lactiplantibacillus plantarum / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D010641:Phenotype; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial