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Applied and Environmental Microbiology Jul 2005We describe a simple colony overlay procedure for peptidases (COPP) for the rapid fluorogenic detection and quantification of Vibrionaceae from seawater, shellfish,...
We describe a simple colony overlay procedure for peptidases (COPP) for the rapid fluorogenic detection and quantification of Vibrionaceae from seawater, shellfish, sewage, and clinical samples. The assay detects phosphoglucose isomerase with a lysyl aminopeptidase activity that is produced by Vibrionaceae family members. Overnight cultures are overlaid for 10 min with membranes containing a synthetic substrate, and the membranes are examined for fluorescent foci under UV illumination. Fluorescent foci were produced by all the Vibrionaceae tested, including Vibrio spp., Aeromonas spp., and Plesiomonas spp. Fluorescence was not produced by non-Vibrionaceae pathogens. Vibrio cholerae strains O1, O139, O22, and O155 were strongly positive. Seawater and oysters were assayed, and 87 of 93 (93.5%) of the positive isolates were identified biochemically as Vibrionaceae, principally Vibrio vulnificus, Vibrio parahaemolyticus, Aeromonas hydrophila, Photobacterium damselae, and Shewanella putrefaciens. None of 50 nonfluorescent isolates were Vibrionaceae. No Vibrionaceae were detected in soil, and only A. hydrophila was detected in sewage. The COPP technique may be particularly valuable in environmental and food-testing laboratories and for monitoring water quality in the aquaculture industry.
Topics: Animals; Bacterial Typing Techniques; Coumarins; Culture Media; Dipeptides; Fluorescence; Gram-Negative Bacterial Infections; Humans; Ostreidae; Peptide Hydrolases; Seawater; Sewage; Shellfish; Time Factors; Vibrionaceae
PubMed: 16000757
DOI: 10.1128/AEM.71.7.3524-3527.2005 -
PloS One 2012Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low... (Comparative Study)
Comparative Study
Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low temperatures as well as a higher viscosity of the aqueous environment require certain adaptations to the metabolic machinery of the cell. In addition to this, low temperature has deleterious effects on the lipid bilayer of bacterial membranes and therefore might also affect the embedded membrane proteins. Little is known about the adaptation of membrane proteins to stresses of the cold. In this study we investigate a set of 66 membrane proteins from the core genome of the bacterial family Vibrionaceae to identify general characteristics that discern psychrophilic and mesophilic membrane proteins. Bioinformatical and statistical methods were used to analyze the alignments of the three temperature groups mesophilic, intermediate and psychrophilic. Surprisingly, our results show little or no adaptation to low temperature for those parts of the proteins that are predicted to be inside the membrane. However, changes in amino acid composition and hydrophobicity are found for complete sequences and sequence parts outside the lipid bilayer. Among others, the results presented here indicate a preference for helix-breaking and destabilizing amino acids Ile, Asp and Thr and an avoidance of the helix-forming amino acid Ala in the amino acid composition of psychrophilic membrane proteins. Furthermore, we identified a lower overall hydrophobicity of psychrophilic membrane proteins in comparison to their mesophilic homologs. These results support the stability-flexibility hypothesis and link the cold-adaptation strategies of membrane proteins to those of loop regions of psychrophilic enzymes.
Topics: Adaptation, Physiological; Bacterial Proteins; Cold Temperature; Computational Biology; Genome, Bacterial; Hydrophobic and Hydrophilic Interactions; Membrane Proteins; Vibrionaceae
PubMed: 23284762
DOI: 10.1371/journal.pone.0051761 -
Journal of Clinical Microbiology Apr 1986Sixty isolates, comprising nine species of the family Vibrionaceae, were tested with the API 20E 5-h same-day procedure (Analytab Products, Plainview, N.Y.). Included...
Sixty isolates, comprising nine species of the family Vibrionaceae, were tested with the API 20E 5-h same-day procedure (Analytab Products, Plainview, N.Y.). Included were 27 Aeromonas hydrophila isolates, 10 Aeromonas sobria isolates, 7 Aeromonas caviae isolates, 3 Plesiomonas shigelloides isolates, 3 Vibrio alginolyticus isolates, 3 Vibrio cholerae isolates, 1 Vibrio fluvialis isolate, 5 Vibrio parahaemolyticus isolates, and 1 Vibrio vulnificus isolate. The 5-h profile numbers were specific for the five Vibrio species and the Plesiomonas isolates. The three Aeromonas species shared seven 5-h profile numbers. Of the 63 5-h profile numbers generated by testing each isolate twice, 22 were identical to those found in the overnight analytical profile index. Of these, 20 were correct identifications, and two were incorrect. The remaining 41 5-h profile numbers were not found in the overnight analytical profile index. Because the 5-h analytical profile index does not contain any oxidase-positive organisms, the oxidase value was subtracted from the 63 5-h profile numbers to determine whether misidentifications could occur if the oxidase test was either not performed or not performed correctly. Only five of these factored profile numbers resulted in a possible misidentification. It is feasible, within limitations, to use the 5-h API 20E same-day procedure to identify the more commonly occurring members of the Vibrionaceae. The manufacturer should develop a data base for this purpose.
Topics: Aeromonas; Bacteriological Techniques; Information Systems; Vibrio; Vibrio cholerae; Vibrio parahaemolyticus; Vibrionaceae
PubMed: 3517061
DOI: 10.1128/jcm.23.4.715-717.1986 -
Molecular Microbiology Aug 2013Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to...
Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to acquire new traits that can enhance their fitness in different environments. Within the past decade, numerous studies have revealed that natural transformation is prevalent among members of the Vibrionaceae, including the pathogen Vibrio cholerae. Four environmental factors: (i) nutrient limitation, (ii) availability of extracellular nucleosides, (iii) high cell density and (iv) the presence of chitin, promote genetic competence and natural transformation in Vibrio cholerae by co-ordinating expression of the regulators CRP, CytR, HapR and TfoX respectively. Studies of other Vibrionaceae members highlight the general importance of natural transformation within this bacterial family.
Topics: DNA Transformation Competence; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Recombination, Genetic; Transformation, Bacterial; Vibrionaceae
PubMed: 23803158
DOI: 10.1111/mmi.12307 -
Microbial Ecology Jan 2010Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved...
Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.
Topics: DNA Fingerprinting; Evolution, Molecular; Genome, Bacterial; Phylogeny; RNA, Ribosomal, 16S; Vibrio; Vibrio cholerae; Vibrionaceae
PubMed: 19830476
DOI: 10.1007/s00248-009-9596-7 -
International Journal of Systematic... Jan 1993The phylogenetic relationships of 50 reference strains, mostly marine bacteria which require Na+ for growth, were determined on the basis of 600 16S rRNA nucleotides by... (Comparative Study)
Comparative Study
The phylogenetic relationships of 50 reference strains, mostly marine bacteria which require Na+ for growth, were determined on the basis of 600 16S rRNA nucleotides by using reverse transcriptase sequencing. Strains belonging to 10 genera were included (four genera of the family Vibrionaceae, the genus Aeromonas of the family Aeromonadaceae, and the genera Alteromonas, Marinomonas, Shewanella, Pseudomonas, and Deleya). The sequences were aligned, the similarity values and evolutionary distance values were determined, and a phylogenetic tree was constructed by using the neighbor-joining method. On the basis of our results, the family Vibrionaceae was separated into at least seven groups (genera and families). Vibrio marinus clearly was on a line of descent that was remote from other vibrios. As determined by the similarity and evolutionary distance values, V. marinus is more distantly related to the family Vibrionaceae than the members of the Aeromonadaceae are. Also, Vibrio cholerae strains formed a separate group with Vibrio mimicus at the genus level. Of 30 species of the Vibrionaceae, 17 formed a large phylogenetic cluster. The genus Listonella was found to be a heterogeneous group, and the species were distributed in various subgroups of the Vibrionaceae. The separation of the family Aeromonadaceae from the family Vibrionaceae and the separation of the genera Marinomonas and Shewanella from the genus Alteromonas were confirmed in this phylogenetic study. However, a marine Pseudomonas species, Pseudomonas nautica, was clearly separated from two terrestrial Pseudomonas species. Each group that was separated by the phylogenetic analysis had characteristic 16S rRNA sequence patterns that were common only to species in that group. Therefore, the characteristic sequences described in this paper may be useful for identification purposes.
Topics: Base Sequence; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Homology, Nucleic Acid; Vibrionaceae; Water Microbiology
PubMed: 8427811
DOI: 10.1099/00207713-43-1-8 -
BMC Genomics Jun 2010Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence... (Comparative Study)
Comparative Study
BACKGROUND
Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges.
RESULTS
We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes) and 5,584 unique proteins (encoded once on only one of the eleven genomes). Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined.
CONCLUSIONS
The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.
Topics: Bacterial Proteins; Evolution, Molecular; Genes, Bacterial; Genetic Variation; Genomics; Proteome; Sequence Homology, Amino Acid; Species Specificity; Vibrionaceae
PubMed: 20537180
DOI: 10.1186/1471-2164-11-369 -
BMC Genomics May 2012The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more...
BACKGROUND
The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.
RESULTS
The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.
CONCLUSION
The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.
Topics: Adaptation, Biological; Cluster Analysis; Databases, Genetic; Gene Transfer, Horizontal; Genome, Bacterial; Multigene Family; Phylogeny; Software; Species Specificity; Vibrionaceae
PubMed: 22574681
DOI: 10.1186/1471-2164-13-179 -
International Journal of Systematic and... Jan 2005Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment...
Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA-DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family Vibrionaceae.
Topics: Algorithms; Bacterial Typing Techniques; DNA Fingerprinting; Genotype; Polymorphism, Restriction Fragment Length; Software; Stochastic Processes; Vibrionaceae
PubMed: 15653853
DOI: 10.1099/ijs.0.63136-0 -
Applied and Environmental Microbiology Oct 2011We synthesized population structure data from three studies that assessed the fine-scale distribution of Vibrionaceae among temporally and spatially distinct... (Comparative Study)
Comparative Study
We synthesized population structure data from three studies that assessed the fine-scale distribution of Vibrionaceae among temporally and spatially distinct environmental categories in coastal seawater and animals. All studies used a dynamic model (AdaptML) to identify phylogenetically cohesive and ecologically distinct bacterial populations and their predicted habitats without relying on a predefined genetic cutoff or relationships to previously named species. Across the three studies, populations were highly overlapping, displaying similar phylogenetic characteristics (identity and diversity), and were predominantly congruent with taxonomic Vibrio species previously characterized as genotypic clusters by multilocus sequence analysis (MLSA). The environmental fidelity of these populations appears high, with 9 out of 12 reproducibly associating with the same predicted (micro)habitats when similar environmental categories were sampled. Overall, this meta-analysis provides information on the habitat predictability and structure of previously described species, demonstrating that MLSA-based taxonomy can, at least in some cases, serve to approximate ecologically cohesive populations.
Topics: Animals; Bacterial Proteins; Classification; Cluster Analysis; DNA, Bacterial; Ecology; Ecosystem; Environmental Microbiology; Gram-Negative Bacterial Infections; Molecular Sequence Data; Phylogeny; Sequence Analysis, DNA; Vibrionaceae
PubMed: 21873482
DOI: 10.1128/AEM.00665-11