Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida

Abstract

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...

Comparative Genomic Analysis of Vibrio diabolicus and Six Taxonomic Synonyms: A First Look at the Distribution and Diversity of the Expanded Species

“…The entirety of the tree, without collapsed branches, was included in the Supplementary Figure S1 . This phylogeny showed strong agreement with previous whole-genome Harveyi clade phylogenies ( Thompson et al, 2009 ; Lin et al, 2010 ; Urbanczyk et al, 2013 , 2014 , 2016 ; Ke et al, 2017 ), but unlike previous phylogenies, the aim of this phylogeny was the resolution of the non-core Harveyi subclades (e.g., V. alginolyticus, V. antiquarius, V. diabolicus , and V. parahaemolyticus ). To that end, the discovery of a well-supported V. diabolicus subclade comprised of two V. diabolicus strains (Art-Gut C1 and CNCM I-1629), two V. antiquarius strains (939 and EX25) and four V. alginolyticus strains (E0666, FF273, TS13, and V2) was novel.…”

“…In contrast, these genomes shared less than 92% ANI with representative V. alginolyticus genomes, confirming that they are distinct in comparison to their nearest phylogenetic neighbor. A similar study used the 97% ANI threshold to support the conclusion that V. inhibens is a heterotypic synonym of V. jasicida ( Urbanczyk et al, 2016 ). In this study, the analysis of ANI values clearly showed that two V. antiquarius strains (939 and EX25) and four V. alginolyticus strains (E0666, FF273, TS13, and V2) are synonyms of V. diabolicus .…”

“…In particular, species boundaries between members of the Harveyi clade (e.g., V. campbellii, V. harveyi, V. rotiferianus, V. natriegens , and V. parahaemolyticus ) have proven especially difficult to delineate ( Thompson et al, 2006 ). However, the advent of multilocus ( Thompson et al, 2005 , 2007 ; Sawabe et al, 2007 , 2013 ; González-Escalona et al, 2008 ) and genome-scale phylogenetics ( Thompson et al, 2009 ; Lin et al, 2010 ; Urbanczyk et al, 2013 , 2014 , 2016 ; Ke et al, 2017 ) has advanced our understanding of this once enigmatic clade. This study builds on previous work by clarifying the relatedness of two Harveyi clade species first isolated from the deep-sea: V. diabolicus and V. antiquarius .…”

Detection of mcr-1 Gene in Undefined Vibrio Species Isolated from Clams

“…nov. contains similarly mainly 16:0 (14-30%), 18:1 ω7c (8-24%), and summed feature 3 (35-43%) [80]. It has been proposed that V. inhibens is a later heterotypic synonym of V. jasicida [81]. The most curious fatty acid in the three isolates of the present study is the polyunsaturated 18:3 w6c (Table 3).…”

Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade

“…This clade consists of 10 evolutionarily closely related species with validly described names (2,9). Bacteria in the clade are difficult to classify using polyphasic taxonomy and require the use of genomic data to accurately classify strains into species (9)(10)(11)(12). Studies of Harveyi clade Vibrio bacteria allow a good opportunity to compare the delineation of bacteria based on their ecology with the classification using polyphasic taxonomy.…”