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Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and ‘P. mandapamensis’. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of ‘P. mandapamensis’ svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than ‘P. mandapamensis’. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and ‘P. mandapamensis’ found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.

Vibrio inhibens is a marine bacterium species of the genus Vibrio (Vibrionaceae, Gammaproteobacteria). The species has been shown to be closely related to members of the genus Vibrio in the so-called Harveyi clade. The clade includes at least 11 closely related species with similar physiological and biochemical properties. Due to these similarities, species of the Harveyi clade are difficult to characterize taxonomically. Previously phenotypic and genotypic properties of the V. inhibens type strain were compared with six species of the Harveyi clade, resulting in the possibility that V. inhibens could be a synonym of a previously described species. In this study, the taxonomic status of V. inhibens was analyzed using genomic approaches. The whole-genome sequence of the type strain of V. inhibens, CECT 7692 T , was obtained and analyzed. Calculations of average nucleotide identity with the BLAST algorithm (ANIb) showed that CECT 7692 T has an ANIb of 97.5 % or higher to five strains of Vibrio. jasicida, including the type strain, but an ANIb lower than 93.5 % to other members of the Harveyi clade Vibrio. Phylogenetic analysis based on nucleotide sequences of 133 protein-coding genes showed a close evolutionary relationship of CECT 7692 T to V. jasicida. Based on these results, Vibrio inhibens is proposed to be a later heterotypic synonym of V. jasicida.Strain CECT 7692 T was isolated from feces of wild longsnouted seahorse (Hippocampus guttulatus) (Balcazar et al., 2012). Based on a phylogenetic analysis of sequences of five genes, as well as a chemophenotypic analysis the strain was taxonomically classified as representing a novel species of the genus Vibrio (family Vibrionaceae, Gammaproteobacteria), Vibrio inhibens (Balcazar et al., 2012). So far, the species type strain (CECT 7692 T =DSM 23440 T =BFLP-10 T ) is the only strain of V. inhibens described in the literature. The type strain of V. inhibens, CECT 7692 T , was obtained from the Spanish Type Culture Collection (CECT). Genomic DNA of CECT 7692 T was isolated using a DNeasy Blood and Tissue kit (Qiagen). The whole-genome sequence was generated using an Illumina MiSeq platform and a Nextera XT DNA Sample Prep kit (Illumina). Pairedend sequencing resulted in 2 367 933 reads (after quality trimming), which were assembled using Platanus assembler version 1.2.1 with the option for haploid genome (Katijani et al., 2014) into 237 scaffolds of over 300 bp in length, with approximately 132-fold coverage. The draft genome was 5 945 135 bp in length, with a DNA G+C content of 43.82 %. The CECT 7692 T genome sequence was submitted Abbreviations: MLSA, multi-locus sequence analysis; ANI, average nucleotide identity; GGDC, genome-to-genome distance comparison; ANIb, ANI calculated with the blast algorithm; ANIm, ANI calculated with the MUMmer algorithm; orthoANI, orthology ANI .V. inhibens CECT 7692 T 16S rRNA sequence obtained in this study has GenBank accession number KU360274. CECT 7692 T genome sequence has DDBJ accession numbers DF977004 to DF977445.Six supple...

Strain 020920NT was isolated from the estuary of the Kaeda river in the Miyazaki prefecture in Japan. Phylogenetic analysis based on the 16S rRNA gene showed the strain’s close evolutionary relationship with bacteria from the genus Grimontia , in the family Vibrionaceae . Phenotypic and chemotaxonomic features of the strain were investigated. Whole genome sequencing revealed that the strain 020920NT genome consists of two chromosomes and a plasmid, for a total of 5.52 Mbp. Calculations of whole genome average nucleotide identity and phylogenetic analysis based on the whole genome sequence showed that the strain represents a new species in the genus Grimontia , for which we propose the name Grimontia kaedaensis sp. nov. with the type strain 020920NT (=LMG 32507T=JCM 34978T).

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