-
Wiley Interdisciplinary Reviews. RNA 2014In bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial... (Review)
Review
In bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial gene regulation, including control of pathogenicity. The Vibrionaceae constitute a family of marine bacteria of which many are responsible for infections affecting not only humans, such as Vibrio cholerae but also fish and marine invertebrates, representing the major cause of mortality in farmed marine species. They are able to colonize many habitats, existing as planktonic forms, in biofilms or associated with various hosts. This high adaptability is linked to their capacity to generate genetic diversity, in part through lateral gene transfer, but also by varying gene expression control. In the recent years, several major studies have illustrated the importance of small regulatory sRNAs in the Vibrionaceae for the control of pathogenicity and adaptation to environment and nutrient sources such as chitin, especially in V. cholerae and Vibrio harveyi. The existence of a complex regulatory network controlled by quorum sensing has been demonstrated in which sRNAs play central roles. This review covers major advances made in the discovery and elucidation of functions of Vibrionaceae sRNAs within the last 10 years.
Topics: Animals; Evolution, Molecular; Gene Expression Regulation, Bacterial; Gram-Negative Bacterial Infections; Humans; Iron; Quorum Sensing; RNA, Bacterial; RNA, Small Untranslated; Vibrionaceae
PubMed: 24458378
DOI: 10.1002/wrna.1218 -
Microbiology Spectrum Oct 2015Similar to other genera and species of bacteria, whole genomic sequencing has revolutionized how we think about and address questions of basic Vibrio biology. In this... (Review)
Review
Similar to other genera and species of bacteria, whole genomic sequencing has revolutionized how we think about and address questions of basic Vibrio biology. In this review we examined 36 completely sequenced and annotated members of the Vibrionaceae family, encompassing 12 different species of the genera Vibrio, Aliivibrio, and Photobacterium. We reconstructed the phylogenetic relationships among representatives of this group of bacteria by using three housekeeping genes and 16S rRNA sequences. With an evolutionary framework in place, we describe the occurrence and distribution of primary and alternative sigma factors, global regulators present in all bacteria. Among Vibrio we show that the number and function of many of these sigma factors differs from species to species. We also describe the role of the Vibrio-specific regulator ToxRS in fitness and survival. Examination of the biochemical capabilities was and still is the foundation of classifying and identifying new Vibrio species. Using comparative genomics, we examine the distribution of carbon utilization patterns among Vibrio species as a possible marker for understanding bacteria-host interactions. Finally, we discuss the significant role that horizontal gene transfer, specifically, the distribution and structure of integrons, has played in Vibrio evolution.
Topics: Aliivibrio; Animals; Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Evolution, Molecular; Gene Transfer, Horizontal; Genes, Essential; Genes, Regulator; Genetic Variation; Genome, Bacterial; Gram-Negative Bacterial Infections; Host-Pathogen Interactions; Humans; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sigma Factor; Vibrio
PubMed: 26542048
DOI: 10.1128/microbiolspec.VE-0009-2014 -
Archives of Microbiology Nov 2023The marine bacteria of the Vibrionaceae family are significant from the point of view of their role in the marine geochemical cycle, as well as symbionts and... (Review)
Review
The marine bacteria of the Vibrionaceae family are significant from the point of view of their role in the marine geochemical cycle, as well as symbionts and opportunistic pathogens of aquatic animals and humans. The well-known pathogens of this group, Vibrio cholerae, V. parahaemolyticus, and V. vulnificus, are responsible for significant morbidity and mortality associated with a range of infections from gastroenteritis to bacteremia acquired through the consumption of raw or undercooked seafood and exposure to seawater containing these pathogens. Although generally regarded as susceptible to commonly employed antibiotics, the antimicrobial resistance of Vibrio spp. has been on the rise in the last two decades, which has raised concern about future infections by these bacteria becoming increasingly challenging to treat. Diverse mechanisms of antimicrobial resistance have been discovered in pathogenic vibrios, the most important being the membrane efflux pumps, which contribute to antimicrobial resistance and their virulence, environmental fitness, and persistence through biofilm formation and quorum sensing. In this review, we discuss the evolution of antimicrobial resistance in pathogenic vibrios and some of the well-characterized efflux pumps' contributions to the physiology of antimicrobial resistance, host and environment survival, and their pathogenicity.
Topics: Animals; Humans; Anti-Bacterial Agents; Vibrionaceae; Drug Resistance, Bacterial; Vibrio; Vibrio cholerae; Vibrio parahaemolyticus
PubMed: 38017151
DOI: 10.1007/s00203-023-03731-5 -
Nature Reviews. Microbiology Sep 2006The Vibrionaceae show a wide range of niche specialization, from free-living forms to those attached to biotic and abiotic surfaces, from symbionts to pathogens and from... (Comparative Study)
Comparative Study Review
The Vibrionaceae show a wide range of niche specialization, from free-living forms to those attached to biotic and abiotic surfaces, from symbionts to pathogens and from estuarine inhabitants to deep-sea piezophiles. The existence of complete genome sequences for closely related species from varied aquatic niches makes this group an excellent case study for genome comparison.
Topics: Animals; Ecosystem; Genes, Bacterial; Genome, Bacterial; Humans; Phylogeny; Seawater; Sequence Homology, Nucleic Acid; Vibrionaceae
PubMed: 16894340
DOI: 10.1038/nrmicro1476 -
Microbiology and Molecular Biology... Sep 2001Polar flagella of Vibrio species can rotate at speeds as high as 100,000 rpm and effectively propel the bacteria in liquid as fast as 60 microm/s. The sodium motive... (Review)
Review
Polar flagella of Vibrio species can rotate at speeds as high as 100,000 rpm and effectively propel the bacteria in liquid as fast as 60 microm/s. The sodium motive force powers rotation of the filament, which acts as a propeller. The filament is complex, composed of multiple subunits, and sheathed by an extension of the cell outer membrane. The regulatory circuitry controlling expression of the polar flagellar genes of members of the Vibrionaceae is different from the peritrichous system of enteric bacteria or the polar system of Caulobacter crescentus. The scheme of gene control is also pertinent to other members of the gamma purple bacteria, in particular to Pseudomonas species. This review uses the framework of the polar flagellar system of Vibrio parahaemolyticus to provide a synthesis of what is known about polar motility systems of the Vibrionaceae. In addition to its propulsive role, the single polar flagellum of V. parahaemolyticus is believed to act as a tactile sensor controlling surface-induced gene expression. Under conditions that impede rotation of the polar flagellum, an alternate, lateral flagellar motility system is induced that enables movement through viscous environments and over surfaces. Although the dual flagellar systems possess no shared structural components and although distinct type III secretion systems direct the simultaneous placement and assembly of polar and lateral organelles, movement is coordinated by shared chemotaxis machinery.
Topics: Chemotaxis; Flagella; Flagellin; Gene Expression Regulation, Bacterial; Genes, Bacterial; Microscopy, Electron; Vibrionaceae
PubMed: 11528005
DOI: 10.1128/MMBR.65.3.445-462.2001 -
Marine Drugs 2011Bacteria belonging to the Vibrionaceae family are widespread in the marine environment. Today, 128 species of vibrios are known. Several of them are infamous for their... (Review)
Review
Bacteria belonging to the Vibrionaceae family are widespread in the marine environment. Today, 128 species of vibrios are known. Several of them are infamous for their pathogenicity or symbiotic relationships. Despite their ability to interact with eukaryotes, the vibrios are greatly underexplored for their ability to produce bioactive secondary metabolites and studies have been limited to only a few species. Most of the compounds isolated from vibrios so far are non-ribosomal peptides or hybrids thereof, with examples of N-containing compounds produced independent of nonribosomal peptide synthetases (NRPS). Though covering a limited chemical space, vibrios produce compounds with attractive biological activities, including antibacterial, anticancer, and antivirulence activities. This review highlights some of the most interesting structures from this group of bacteria. Many compounds found in vibrios have also been isolated from other distantly related bacteria. This cosmopolitan occurrence of metabolites indicates a high incidence of horizontal gene transfer, which raises interesting questions concerning the ecological function of some of these molecules. This account underlines the pending potential for exploring new bacterial sources of bioactive compounds and the challenges related to their investigation.
Topics: Anti-Bacterial Agents; Ecology; Genetic Variation; Phylogeny; Quorum Sensing; Siderophores; Vibrionaceae
PubMed: 22131950
DOI: 10.3390/md9091440 -
Research in Microbiology 2007Despite the broad diversity of Vibrionaceae, they display a surprising number of conserved features, most striking of which may be the ubiquitous presence of two... (Review)
Review
Despite the broad diversity of Vibrionaceae, they display a surprising number of conserved features, most striking of which may be the ubiquitous presence of two chromosomes. Based on complete genome sequences and the findings generated therefrom, we discuss the origin, evolution and stability of this unusual chromosomal arrangement as well as its possible benefits.
Topics: Chromosomes, Bacterial; DNA Replication; DNA, Bacterial; Evolution, Molecular; Gene Dosage; Gene Rearrangement; Genetic Variation; Vibrionaceae
PubMed: 17590316
DOI: 10.1016/j.resmic.2007.04.007 -
Current Genetics Feb 2016Many proteobacteria modulate a suite of catabolic genes using the second messenger cyclic 3', 5'-AMP (cAMP) and the cAMP receptor protein (CRP). Together, the cAMP-CRP... (Review)
Review
Many proteobacteria modulate a suite of catabolic genes using the second messenger cyclic 3', 5'-AMP (cAMP) and the cAMP receptor protein (CRP). Together, the cAMP-CRP complex regulates target promoters, usually by activating transcription. In the canonical model, the phosphotransferase system (PTS), and in particular the EIIA(Glc) component for glucose uptake, provides a mechanistic link that modulates cAMP levels depending on glucose availability, resulting in more cAMP and activation of alternative catabolic pathways when glucose is unavailable. Within the Vibrionaceae, cAMP-CRP appears to play the classical role in modulating metabolic pathways; however, it also controls functions involved in natural competence, bioluminescence, pheromone signaling, and colonization of animal hosts. For this group of marine bacteria, chitin is an ecologically relevant resource, and chitin's monomeric sugar N-acetylglucosamine (NAG) supports robust growth while also triggering regulatory responses. Recent studies with Vibrio fischeri indicate that NAG and glucose uptake share EIIA(Glc), yet the responses of cAMP-CRP to these two carbon sources are starkly different. Moreover, control of cAMP levels appears to be more dominantly controlled by export and degradation. Perhaps more surprisingly, although CRP may require cAMP, its activity can be controlled in response to glucose by a mechanism independent of cAMP levels. Future studies in this area promise to shed new light on the role of cAMP and CRP.
Topics: Carbohydrate Metabolism; Cyclic AMP; Cyclic AMP Receptor Protein; Glucose; Vibrionaceae
PubMed: 26215147
DOI: 10.1007/s00294-015-0508-8 -
Current Microbiology Dec 2021Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of...
Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
Topics: Base Sequence; Genome, Bacterial; Phylogeny; Sequence Analysis, DNA; Vibrio; Vibrionaceae
PubMed: 34905112
DOI: 10.1007/s00284-021-02725-0 -
Environmental Science and Pollution... Sep 2022The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of...
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
Topics: Animals; Ecosystem; Environmental Monitoring; Genes, rRNA; Humans; Particulate Matter; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sewage; Vibrionaceae; Wastewater; Water
PubMed: 36056283
DOI: 10.1007/s11356-022-22752-z