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BMC Genomics Oct 2020The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork...
BACKGROUND
The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.
RESULTS
We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.
CONCLUSION
The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.
Topics: Chromosome Mapping; Chromosomes, Bacterial; Genes, Bacterial; Vibrionaceae
PubMed: 33023476
DOI: 10.1186/s12864-020-07117-5 -
BMC Genomics Jun 2020In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool...
BACKGROUND
In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (N), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.
RESULTS
We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high N estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.
CONCLUSIONS
Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.
Topics: Adaptation, Physiological; Gene Transfer, Horizontal; Genetics, Population; Genome, Bacterial; Multigene Family; Mutation; Phylogeny; Polymorphism, Single Nucleotide; Population Density; Selection, Genetic; Vibrionaceae; Whole Genome Sequencing
PubMed: 32571204
DOI: 10.1186/s12864-020-06829-y -
Journal of Aquatic Animal Health Dec 2019In this study, levels of Vibrionaceae, Staphylococcaceae, and Enterobacteriaceae were observed in seawater from juvenile green turtle Chelonia mydas rearing tanks and in...
In this study, levels of Vibrionaceae, Staphylococcaceae, and Enterobacteriaceae were observed in seawater from juvenile green turtle Chelonia mydas rearing tanks and in the incoming coastal seawater (the water supply). Bacterial loads were compared between the incoming coastal seawater and two different rearing conditions: in cement tanks at a low stocking density and in fiberglass tanks at a high stocking density. The total bacterial counts in seawater from fiberglass tanks were statistically greater than those in cement tanks. The nonlactose and lactose fermenting enterobacteria, tellurite-reducing bacteria, and total plate counts in water from all rearing containers were greater than those in coastal seaweater by a logarithmic fold change of 2--3. Differences in bacterial population structure of the incoming coastal seawater and rearing water were also addressed. The results from biochemical identification of 344 isolates revealed that the bacteria that were commonly found in water samples were Citrobacter spp., Enterobacteria spp., Edwardsiella spp., Staphylococcus spp., Staphylococcus aureus, Photobacterium spp., Vibrio alginolyticus, and Vibrio spp. Conclusively, the microbiological monitoring of rearing water provides important and essential information on the management of aquatic animal health and husbandry.
Topics: Animals; Animals, Zoo; Enterobacteriaceae; Seawater; Staphylococcaceae; Thailand; Turtles; Vibrionaceae
PubMed: 31342564
DOI: 10.1002/aah.10082 -
Microbial Genomics Apr 2023is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second,...
is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in and non- species, suggesting that the T3SS2 gene cluster is not restricted to the and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the T3SS2 gene cluster.
Topics: Humans; Type III Secretion Systems; Vibrionaceae; Phylogeny; Vibrio Infections; Vibrio parahaemolyticus
PubMed: 37018030
DOI: 10.1099/mgen.0.000973 -
Annual Review of Microbiology 1977
Review
Topics: Adenosine Triphosphate; Aldehydes; Anesthetics; Arginine; Bacteriophages; Chemical Phenomena; Chemistry; Cyclic AMP; Flavin Mononucleotide; Genes; Genetic Variation; Luciferases; Luminescent Measurements; Mutation; NAD; Oxygen Consumption; Photobacterium; Pyruvates; Sodium Chloride; Vibrio; Vibrionaceae
PubMed: 199107
DOI: 10.1146/annurev.mi.31.100177.003001 -
Environmental Research Feb 2023Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of...
Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of coastal waters is increasing the abundance and virulence of pathogenic members of the Vibrionaceae, posing a significant health risk to both humans and aquatic organisms. Fish disease, notably outbreaks of emerging pathogens in response to environmental perturbations such as heatwaves, have been recognised in aquaculture settings. Considerably less is known about how rising sea surface temperatures will impact the microbiology of wild fish populations, particularly those within estuarine systems that are more vulnerable to warming. We used a combination of Vibrio-specific quantitative PCR and amplicon sequencing of the 16S rRNA and hsp60 genes to examine seawater and fish (Pelates sexlineatus) gut microbial communities across a quasi-natural experimental system, where thermal pollution from coal-fired power stations creates a temperature gradient of up to 6 °C, compatible with future predicted temperature increases. At the warmest site, fish hindgut microbial communities were in a state of dysbiosis characterised by shifts in beta diversity and a proliferation (71.5% relative abundance) of the potential fish pathogen Photobacterium damselae subsp. damselae. Comparable patterns were not identified in the surrounding seawater, indicating opportunistic proliferation within estuarine fish guts under thermal stress. A subsequent evaluation of predicted future warming-related risk due to pathogenic Vibrionaceae in temperate estuarine fish demonstrated that warming is likely to drive opportunistic pathogen increases in the upper latitudinal range of this estuarine fish, potentially impacting adaptations to future warming. These findings represent a breakthrough in our understanding of the dynamics of emerging pathogens in populations of wild aquatic organisms within environments likely to experience rapid warming under future climate change.
Topics: Animals; Humans; Aquatic Organisms; Australia; Dysbiosis; Estuaries; Fishes; RNA, Ribosomal, 16S; Temperature; Vibrionaceae; Water; Intestines
PubMed: 36584839
DOI: 10.1016/j.envres.2022.115144 -
Environmental Microbiology Oct 2022The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular...
The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible for their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that (1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements; (2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; (3) different carbohydrate degradation preferences may be the result of environmental adaptation; and (4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes.
Topics: Animals; Carbohydrates; Evolution, Molecular; Genome, Bacterial; Phylogeny; Vibrionaceae; Virulence; Virulence Factors; Genome
PubMed: 36106979
DOI: 10.1111/1462-2920.16209 -
FEMS Microbiology Ecology Mar 2021Deciphering the cues that stimulate microorganisms to produce their full secondary metabolic potential promises to speed up the discovery of novel drugs....
Deciphering the cues that stimulate microorganisms to produce their full secondary metabolic potential promises to speed up the discovery of novel drugs. Ecology-relevant conditions, including carbon-source(s) and microbial interactions, are important effectors of secondary metabolite production. Vice versa secondary metabolites are important mediators in microbial interactions, although their exact natural functions are not always completely understood. In this study, we investigated the effects of microbial interactions and in-culture produced antibiotics on the production of secondary metabolites by Vibrio coralliilyticus and Photobacterium galatheae, two co-occurring marine Vibrionaceae. In co-culture, production of andrimid by V. coralliilyticus and holomycin by P. galatheae, were, compared to monocultures, increased 4.3 and 2.7 fold, respectively. Co-cultures with the antibiotic deficient mutant strains (andrimid- and holomycin-) did not reveal a significant role for the competitor's antibiotic as stimulator of own secondary metabolite production. Furthermore, we observed that V. coralliilyticus detoxifies holomycin by sulphur-methylation. Results presented here indicate that ecological competition in Vibrionaceae is mediated by, and a cue for, antibiotic secondary metabolite production.
Topics: Anti-Bacterial Agents; Photobacterium; Vibrio; Vibrionaceae
PubMed: 33693627
DOI: 10.1093/femsec/fiab041 -
Ugeskrift For Laeger Jul 1989Infections caused by marine vibrios appear to be an increasing problem. Gastroenteritis, soft tissue-infection and septicaemia are the most prevalent manifestations.... (Review)
Review
Infections caused by marine vibrios appear to be an increasing problem. Gastroenteritis, soft tissue-infection and septicaemia are the most prevalent manifestations. Different environmental and traditional water quality measurements do not indicate the risk. These infections are confined to the summer and late summer with water temperatures exceeding 20 degrees C. Tourists may be exposed to an extraordinary risk, and infections may not become apparent until they have returned home. High risk groups (e.g. immunocompromized) have a high case-fatality rate. The extremely rapid onset of these infections demand aggressive antibiotic therapy and vigorous debridement at an early stage. Gastrointestinal disorders may necessitate fluid replacement and tetracycline is recommended in severe cases.
Topics: Denmark; Humans; Risk Factors; Seawater; Vibrio Infections; Vibrionaceae; Water Microbiology
PubMed: 2675436
DOI: No ID Found -
BMC Genomics Jul 2009The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely...
BACKGROUND
The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the exploration of the mechanisms underlying genome plasticity. The family Vibrionaceae is found in the Gammaproteobacteria and is abundant in aquatic environments. Taxa from the family Vibrionaceae are diversified in their life styles; some species are free living, others are symbiotic, and others are human pathogens. This diversity makes this family a useful set of model organisms for studying bacterial evolution. This evolution is driven by several forces, among them gene duplication and lateral gene transfer, which are believed to provide raw material for functional redundancy and novelty. The resultant gene copy increase in one genome is then detected as lineage-specific expansion (LSE).
RESULTS
Here we present the results of a detailed comparison of the genomes of eleven Vibrionaceae strains that have distinct life styles and distinct phenotypes. The core genome shared by all eleven strains is composed of 1,882 genes, which make up about 31%-50% of the genome repertoire. We further investigated the distribution and features of genes that have been specifically expanded in one unique lineage of the eleven strains. Abundant duplicate genes have been identified in the eleven Vibrionaceae strains, with 1-11% of the whole genomes composed lineage specific radiations. These LSEs occurred in two distinct patterns: the first type yields one or more copies of a single gene; we call this a single gene expansion. The second pattern has a high evolutionary impact, as the expansion involves two or more gene copies in a block, with the duplicated block located next to the original block (a contiguous block expansion) or at some distance from the original block (a discontiguous block expansion). We showed that LSEs involve genes that are tied to defense and pathogenesis mechanisms as well as in the fundamental life cycle of Vibrionaceae species.
CONCLUSION
Our results provide evidence of genome plasticity and rapid evolution within the family Vibrionaceae. The comparisons point to sources of genomic variation and candidates for lineage-specific adaptations of each Vibrionaceae pathogen or nonpathogen strain. Such lineage specific expansions could reveal components in bacterial systems that, by their enhanced genetic variability, can be tied to responses to environmental challenges, interesting phenotypes, or adaptive pathogenic responses to host challenges.
Topics: Comparative Genomic Hybridization; Evolution, Molecular; Genome, Bacterial; Sequence Alignment; Sequence Analysis, DNA; Species Specificity; Vibrionaceae
PubMed: 19594870
DOI: 10.1186/1471-2164-10-S1-S11