Vibrio2005: the First International Conference on the Biology of Vibrios

Pan-Genome Provides Insights into Vibrio Evolution and Adaptation to Deep-Sea Hydrothermal Vents

This study delves into the genomic features of 10 Vibrio strains collected from deep-sea hydrothermal vents in the Pacific Ocean, providing insights into their evolutionary history and ecological adaptations. Through sequencing and pan-genome analysis involving 141 Vibrio species, we found that deep-sea strains exhibit larger genomes with unique gene distributions, suggesting adaptation to the vent environment. The phylogenomic reconstruction of the investigated isolates revealed the presence of 2 main clades: The first is monophyletic, consisting exclusively of Vibrio alginolyticus, while the second forms a monophyletic clade comprising both Vibrio antiquarius and Vibrio diabolicus species, which were previously isolated from deep-sea vents. All strains carry virulence and antibiotic resistance genes related to those found in human pathogenic Vibrio species which may play a wider ecological role other than host infection in these environments. In addition, functional genomic analysis identified genes potentially related to deep-sea survival and stress response, alongside candidate genes encoding for novel antimicrobial agents. Ultimately, the pan-genome we generated represents a valuable resource for future studies investigating the taxonomy, evolution, and ecology of Vibrio species.

Development of Recombinant Dihydrolipoamide Dehydrogenase Subunit Vaccine against Vibrio Infection in Large Yellow Croaker

Large yellow croaker (Larimichthys crocea), an economically important marine fish in China, has suffered from serious vibriosis, which has resulted in great economic losses for the large yellow croaker industry. Vaccination has been considered to be a safe and effective method to prevent and control vibriosis. However, due to the complex diversity and serotypes of the Vibrio genus, the progress of Vibrio vaccine development is still slow. In this study, we prepared recombinant Vibrio dihydrolipoamide dehydrogenase (rDLD) protein and investigated its potential as a candidate to be a subunit vaccine against Vibrio. The lysozyme activity and the rDLD-specific antibody level in sera of large yellow croakers immunized with rDLD were significantly higher than those in the control group, and the transcript levels of proinflammatory cytokines (IL-6, IL-8, IL-1β), MHC IIα/β, CD40, CD8α, IL-4/13A, and IL-4/13B were significantly up-regulated in the spleen and head kidney of large yellow croakers immunized with rDLD, suggesting that rDLD could induce both specific and nonspecific immune responses in this species. In addition, rDLD protein increased the survival rate of large yellow croakers against Vibrio alginolyticus and Vibrio parahaemolyticus, with the relative percent of survival (RPS) being 74.5% and 66.9%, respectively. These results will facilitate the development of a potential subunit vaccine against Vibrio in large yellow croaker aquaculture.

Current and future perspectives for controlling Vibrio biofilms in the seafood industry: a comprehensive review

The contamination of seafood with Vibrio species can have severe repercussions in the seafood industry. Vibrio species can form mature biofilms and persist on the surface of several seafoods such as crabs, oysters, mussels, and shrimp, for extended duration. Several conventional approaches have been employed to inhibit the growth of planktonic cells and prevent the formation of Vibrio biofilms. Since Vibrio biofilms are mostly resistant to these control measures, novel alternative methods need to be urgently developed. In this review, we propose environmentally friendly approaches to suppress Vibrio biofilm formation using a hypothesized mechanism of action.

Genetic Relationship, Virulence Factors, Drug Resistance Profile and Biofilm Formation Ability of Vibrio parahaemolyticus Isolated From Mussel

The objective of this study was to investigate the virulence factors, genetic relationship, antibiotic resistance profile and the biofilm formation ability of Vibrio parahaemolyticus isolates on shrimp and mussel surfaces at 30°C. In this study, eight (n = 8) V. parahaemolyticus isolated from mussel were examined. We used the polymerase chain reaction (PCR) to examine the distribution of different genes, and Repetitive Extragenic Palindromic-PCR (REP-PCR) to compare the genetic relationship. Disk diffusion technique was used to assess antibiotic and multiple-antibiotic resistance. The biofilm formation assay, and field emission scanning electron microscopy (FE-SEM) were used to evaluate biofilm formation ability. Transmission Electron Microscope (TEM) was used to observe the morphological structure of bacterial cell. Our results indicated that the biofilm-associated genes, 16S rRNA, toxR, and tdh, were present in all the tested V. parahaemolyticus isolates (n = 8). Approximately, 62.5% (5 isolates among 8 isolates) isolates showed strong multiple-antibiotic resistance index with an average value of 0.56. All isolates (n = 8) showed strong genetic relationship and significant biofilm formation ability on shrimp and mussel surfaces. This study demonstrated that the presence of virulence factors, high multiple antibiotic resistance index (MARI) values, and effective biofilm formation ability of V. parahaemolyticus isolates could be a great threat to human health and economic values in future. It was also suggested that a high resistance rate to antibiotic could be ineffective for treating V. parahaemolyticus infections. The continuous monitoring of V. parahaemolyticus antibiotic, molecular and biofilm characteristics is needed to increase seafood safety.

Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum

Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes. Identification of specific genes, such as N6-adenine methyltransferase and lambda like repressor, as well as the presence of a tRNAArg, suggested a both mutualistic and parasitic interaction between phages and hosts. During short term phage exposure experiments, 28% of a V. anguillarum host population was lysogenized by the temperate phages and a genomic analysis of a collection of 31 virulent V. anguillarum showed that the isolated phages were present as prophages in >50% of the strains covering large geographical distances. Further, phage sequences were widely distributed among CRISPR-Cas arrays of publicly available sequenced Vibrios. The observed distribution of these specific temperate Vibriophages across large geographical scales may be explained by efficient dispersal of phages and bacteria in the marine environment combined with a mutualistic interaction between temperate phages and their hosts which selects for co-existence rather than arms race dynamics.

Evaluation of ToxA and Vibrio parahaemolyticus lysate on humoral immune response and immune-related genes in Pacific red snapper

Immunogenicity of ToxA and Vibrio parahaemolyticus lysate was evaluated in a double immunostimulation scheme in Pacific red snapper after V. parahaemolyticus infection. Three groups of Pacific red snapper were intraperitonealy (i.p.) injected with phosphate-buffered saline (PBS group), ToxA of V. parahaemolyticus (ToxA-Vp group) or V. parahaemolyticus lysate (lysate-Vp group) (first injection, day 1; second injection, day 7). Fish were subsequently infected with live V. parahaemolyticus. Humoral immune parameters in skin mucus and serum were evaluated on days 1, 7, 8 and 14 days post-immunostimulation and 7 days post-infection. Moreover expression of immune-related genes was quantified by real time PCR in head-kidney leukocytes, spleen, liver, and intestine. The ToxA-Vp-treated group showed a higher anti-protease and catalase activity in skin mucus when compared with the PBS group. Measurements of SOD and CAT activities showed an increment in both activities a day after the second boost with ToxA-Vp or lysate-Vp. Interestingly, IgM levels in mucus and transcripts were enhanced followed the ToxA-Vp treatment even after challenge. Furthermore, IL-1β was strongly expressed in all analyzed cell or tissues followed ToxA-Vp or Vp-lysate treatments. Finally, SOD and CAT gene expression was up-regulated in fish immunostimulated with either treatment ToxA-Vp or lysate-Vp, mainly after infection in head-kidney leukocytes and intestine. This is the first study where the effects of ToxA from V. parahaemolyticus in the immune system of Pacific red snapper was evaluated. These results suggest that ToxA-Vp would positively affect humoral immune response and up-regulate expression of genes involved in the immune system function; and could help in the control of V. parahaemolyticus infection in Pacific red snapper Lutjanus peru, an economic important fish in Mexico.

Identification of DLD, by immunoproteomic analysis and evaluation as a potential vaccine antigen against three Vibrio species in Epinephelus coioides

Vibrio spp. represent a serious threat to the culture of Epinephelus coioides (Orange-spotted Grouper) in Southeast Asia. In this study we used two-dimensional electrophoresis (2-DE) and Western blotting to identify common immunogenic proteins of Vibrio alginolyticus, Vibrio harveyi and Vibrio parahaemolyticus. Membranes were probed with orange-spotted grouper anti-V. alginolyticus sera and accordingly 60, 58 and 48 immunogenic protein spots were detected. By matching analysis for the three Western blotting membranes, 6 cross immunogenic spots for the three Vibrio species were identified. They were Outer membrane protein W (OmpW), dihydrolipoamide dehydrogenase (DLD), succinate dehydrogenase flavoprotein subunit(SDHA), elongation factor Ts(Ts), peptide ABC transporter periplasmic peptide-binding protein and phosphoenolpyruvate carboxykinase(PEPCK). One of the proteins, DLD, was used to evaluate the cross protective function for E. coioides with a bacterial immunization and challenge method. The relative percent survival rate of E. coioides against V. alginolyticus, V. harveyi and V. parahaemolyticus was 90%, 86% and 80%, respectively. This work may provide potential cross protective vaccine candidate antigens for three Vibrio species, and DLD may be considered as an effective cross-protective immunogen against three Vibrio species.

Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota

Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.

Identification of capsule, biofilm, lateral flagellum, and type IV pili in Vibrio mimicus strains

Vibrio mimicus is a bacterium that causes gastroenteritis; it is closely related to Vibrio cholerae, and can cause acute diarrhea like cholera- or dysentery-type diarrhea. It is distributed worldwide. Factors associated with virulence (such as hemolysins, enterotoxins, proteases, phospholipases, aerobactin, and hemagglutinin) have been identified; however, its pathogenicity mechanism is still unknown. In pathogenic Vibrio species such as V. cholerae, Vibrio. parahaemolyticus and Vibrio vulnificus, capsule, biofilms, lateral flagellum, and type IV pili are structures described as essential for pathogenicity. These structures had not been described in V. mimicus until this work. We used 20 V. mimicus strains isolated from water (6), oyster (9), and fish (5) samples and we were able to identify the capsule, biofilm, lateral flagellum, and type IV pili through phenotypic tests, electron microscopy, PCR, and sequencing. In all tested strains, we observed and identified the presence of capsular exopolysaccharide, biofilm formation in an in vitro model, as well as swarming, multiple flagellation, and pili. In addition, we identified homologous genes to those described in other bacteria of the genus in which these structures have been found. Identification of these structures in V. mimicus is a contribution to the biology of this organism and can help to reveal its pathogenic behavior.

The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River Estuary, China

Background

The emergence, resurgence and spread of human food-borne pathogenic Vibrios are one of the major contributors to disease burden and mortality particularly in developing countries with disputable sanitary conditions. Previous research on pathogenic Vibrio cholerae and Vibrio parahaemolitycus derived from clinical samples has proposed links between acquisition of virulence and multiple drug resistance traits and intercellular transmissibility of mobile genetic elements in the environment. To date, very few information is available on environmental Vibrio isolates. In this study, we characterized eleven Vibrio strains bearing the SXT/R391-like integrative and conjugative elements (ICEs) derived from aquatic products and environment in the Yangtze River Estuary, China.

Results

The eleven Vibrio strains were isolated in 2010 to 2011, and taxonomically identified, which included six Vibrio cholerae, three Vibrio parahaemolyticus, one Vibrio alginolyticus and one Vibrio natriegens. Most of the strains displayed strong resistance phenotypes to ampicillin, mercury and chromium. The majority of their ICEs, which belong to S and R exclusion system groups, contain ICEs-chromosome junction sequences and highly conserved core-genes required for ICE transfer. However, comparative sequence analysis uncovered interesting diversity in their mosaic accessory gene structures, which carry many novel genes that have not been described in any known ICEs to date. In addition, antibiotic resistance was transmitted by ICEVchChn6 and ICEVpaChn1 from V. cholerae, V. parahaemolyticus to E. coli MG1655 via conjugation, respectively. Our data also revealed that the ICEs characterized in this study are phylogenetically distant from most of the SXT/R391 ICEs reported previously, which may represent a novel cluster likely shaped by the ecological environment in the Yangtze River Estuary, China.

Conclusions

This study constitutes the first investigation of ICEs-positive Vibrio spp. in the Yangze River Estuary, China. The newly identified ICEs were characterized with mosaic accessory gene structures and many novel genes. The results demonstrated self-transmissibility of antibiotic resistance mediated by two of the ICEs from V. cholerae, V. parahaemolyticus to E. coli via conjugation, respectively. Our results also revealed that the ICEs examined in this study may represent a novel cluster in the SXT/R391 family.

TagA is a secreted protease of Vibrio cholerae that specifically cleaves mucin glycoproteins

Vibrio cholerae is a human diarrhoeal pathogen that is a major cause of gastrointestinal disease and death worldwide. Pathogenic V. cholerae strains are characterized by the presence of a Vibrio pathogenicity island (VPI) that encodes virulence factors, including the toxin co-regulated pilus (TCP). TagA is encoded within the VPI and is positively co-regulated with cholera toxin and TCP. TagA is a sequelogue of the StcE mucinase of Escherichia coli O157 : H7. We investigated whether this sequence homology reflected a conserved enzymic substrate profile. TagA exhibited metalloprotease activity toward crude purified mucins, salivary mucin and LS174T goblet cell surface mucin. Like StcE, TagA did not cleave general protease substrates, but unlike StcE, TagA did not cleave the mucin-like serpin C1 esterase inhibitor. Both proteins cleaved the immune cell surface mucin CD43, but TagA demonstrated reduced enzymic efficiency relative to StcE. TagA was expressed and secreted by V. cholerae under ToxR-dependent conditions. A tagA-deficient V. cholerae strain showed no defect in a model of in vitro attachment to the HEp-2 cell line; however, overexpression of a proteolytically inactive mutant, TagA(E433D), caused a significant increase in attachment. The increased attachment was reduced by pretreatment of epithelial monolayers with active TagA. Our results indicate that TagA is a mucinase and suggest that TagA may directly modify host cell surface molecules during V. cholerae infection.

Genomic taxonomy of Vibrios

BACKGROUND

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.

RESULTS

We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree.

CONCLUSION

The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.

Identification of a cellobiose utilization gene cluster with cryptic beta-galactosidase activity in Vibrio fischeri

Cellobiose utilization is a variable trait that is often used to differentiate members of the family Vibrionaceae. We investigated how Vibrio fischeri ES114 utilizes cellobiose and found a cluster of genes required for growth on this beta-1,4-linked glucose disaccharide. This cluster includes genes annotated as a phosphotransferase system II (celA, celB, and celC), a glucokinase (celK), and a glucosidase (celG). Directly downstream of celCBGKA is celI, which encodes a LacI family regulator that represses cel transcription in the absence of cellobiose. When the celCBGKAI gene cluster was transferred to cellobiose-negative strains of Vibrio and Photobacterium, the cluster conferred the ability to utilize cellobiose. Genomic analyses of naturally cellobiose-positive Vibrio species revealed that V. salmonicida has a homolog of the celCBGKAI cluster, but V. vulnificus does not. Moreover, bioinformatic analyses revealed that CelG and CelK share the greatest homology with glucosidases and glucokinases in the phylum Firmicutes. These observations suggest that distinct genes for cellobiose utilization have been acquired by different lineages within the family Vibrionaceae. In addition, the loss of the celI regulator, but not the structural genes, attenuated the ability of V. fischeri to compete for colonization of its natural host, Euprymna scolopes, suggesting that repression of the cel gene cluster is important in this symbiosis. Finally, we show that the V. fischeri cellobioase (CelG) preferentially cleaves beta-d-glucose linkages but also cleaves beta-d-galactose-linked substrates such as 5-bromo-4-chloro-3-indolyl-beta-d-galactoside (X-gal), a finding that has important implications for the use of lacZ as a marker or reporter gene in V. fischeri.

The extracellular metalloprotease of Vibrio tubiashii is a major virulence factor for pacific oyster (Crassostrea gigas) larvae

Vibrio tubiashii is a recently reemerging pathogen of larval bivalve mollusks, causing both toxigenic and invasive disease. Marine Vibrio spp. produce an array of extracellular products as potential pathogenicity factors. Culture supernatants of V. tubiashii have been shown to be toxic to oyster larvae and were reported to contain a metalloprotease and a cytolysin/hemolysin. However, the structural genes responsible for these proteins have yet to be identified, and it is uncertain which extracellular products play a role in pathogenicity. We investigated the effects of the metalloprotease and hemolysin secreted by V. tubiashii on its ability to kill Pacific oyster (Crassostrea gigas) larvae. While V. tubiashii supernatants treated with metalloprotease inhibitors severely reduced the toxicity to oyster larvae, inhibition of the hemolytic activity did not affect larval toxicity. We identified structural genes of V. tubiashii encoding a metalloprotease (vtpA) and a hemolysin (vthA). Sequence analyses revealed that VtpA shared high homology with metalloproteases from a variety of Vibrio species, while VthA showed high homology only to the cytolysin/hemolysin of Vibrio vulnificus. Compared to the wild-type strain, a VtpA mutant of V. tubiashii not only produced reduced amounts of protease but also showed decreased toxicity to C. gigas larvae. Vibrio cholerae strains carrying the vtpA or vthA gene successfully secreted the heterologous protein. Culture supernatants of V. cholerae carrying vtpA but not vthA were highly toxic to Pacific oyster larvae. Together, these results suggest that the V. tubiashii extracellular metalloprotease is important in its pathogenicity to C. gigas larvae.