Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V

Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA.
BMC Microbiology (Impact Factor: 2.73). 05/2010; 10(1):154. DOI: 10.1186/1471-2180-10-154
Source: DOAJ


In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study.
Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp.
Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.

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Available from: Christopher J Grim, Oct 02, 2015
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    • "from both V. cholerae and V. mimicus as well as from the single isolate of the as of yet to be formally described Vibrio sp. RC586 (Haley et al., 2010) (Fig. 1). This further emphasizes the utility of MLSA over the use of the 16S rRNA gene for the identification of species of the genus Vibrio (Pascual et al., 2010; Preheim et al., 2011). "
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    ABSTRACT: A Gram staining negative, curved rod shaped bacterium with close resemblance to Vibrio cholerae, the etiological agent of cholera, was isolated over the course of several years from coastal brackish water (17 strains) and from clinical cases (two strains) in the United States. 16S rRNA gene identity with V. cholerae exceeds 98% yet an average nucleotide identity of around 86% and multi locus sequence analysis of six housekeeping genes (mdh, adk, gyrB, recA, pgi, rpoB) clearly delineates these isolates as a distinct genotypic cluster within the V. cholerae-V. mimicus clade. Most standard identification techniques do not differentiate this cluster of isolates from V. cholerae. Only amplification of the ompW gene using V. cholerae-specific primers and a negative Voges-Proskauer test shows a difference between the two clusters. Additionally, all isolated strains differ phenotypically from V. cholerae in their ability to utilize N-Acetyl-d-galactosamine and d-glucuronic acid as sole carbon sources. Furthermore, they are generally unable to infect the slime mold Dictyostelium discoideum, a widespread ability in V. cholerae. Based on these clear phenotypic differences that are not necessarily apparent in standard tests and, average nucleotide identity and phylogeny of protein-coding genes, we propose the existence of a new species, Vibrio metoecus sp. nov. with the type strain OP3H (LMG 27764, CIP 110643T). Due to its close resemblance to V. cholerae and the increasing number of strains isolated over the past several years, we suggest that V. metoecus sp. nov. is a relatively common Vibrio species that has been identified as atypical isolates of V. cholerae in the past. Its isolation from clinical samples also suggests strains of this species, like V. cholerae, are opportunistic pathogens.
    International Journal of Systematic and Evolutionary Microbiology 06/2014; 64(Pt 9). DOI:10.1099/ijs.0.060145-0 · 2.51 Impact Factor
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    • "These include average nucleotide identity (ANI) (Konstantinidis et al., 2006), genome BLAST distance phylogeny (GBDP) (Henz et al., 2005) and the maximal unique matches index (MUMi) (Deloger et al., 2009). Of these, ANI has been most widely used as a possible next-generation gold standard for species delineation (Chan et al., 2012; Goris et al., 2007; Grim et al., 2013; Haley et al., 2010; Konstantinidis & Tiedje, 2005; Richter & Rosselló -Mó ra, 2009; Yi et al., 2012). ANI represents a mean of identity/similarity values between homologous genomic regions shared by two genomes. "
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    ABSTRACT: Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96 %) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96 % ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65 % 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0 %) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.
    International Journal of Systematic and Evolutionary Microbiology 02/2014; 64(Pt 2):346-51. DOI:10.1099/ijs.0.059774-0 · 2.51 Impact Factor
    • "14 0 Haley et al. (2010) "
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    ABSTRACT: Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA-DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and approaches that can be derived from comparative genomic data and used for taxonomic purposes. Here, an overview about the impact and current usage of ANI values is given together with details of the existing user-friendly package tool, the biology-oriented software package JSpecies, which can be used to generate two types of ANI calculations based on BLAST and MUMmer software packages.
    Methods in Microbiology 01/2014; 41:103-122. DOI:10.1016/bs.mim.2014.07.002 · 0.08 Impact Factor
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