Genomic and systems evolution in Vibrionaceae species

<p>Abstract</p> <p>Background</p> <p>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 <it>Vibrionaceae </it>is found in the <it>Gammaproteobacteria </it>and is abundant in aquatic environments. Taxa from the family <it>Vibrionaceae </it>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).</p> <p>Results</p> <p>Here we present the results of a detailed comparison of the genomes of eleven <it>Vibrionaceae </it>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 <it>Vibrionaceae </it>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 <it>Vibrionaceae </it>species.</p> <p>Conclusion</p> <p>Our results provide evidence of genome plasticity and rapid evolution within the family <it>Vibrionaceae</it>. The comparisons point to sources of genomic variation and candidates for lineage-specific adaptations of each <it>Vibrionaceae </it>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.</p

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Emergence, ecology and dispersal of the pandemic generating Vibrio cholerae lineage

Although cholera is an ancient disease that first arose at least half a millennium ago, it remains a major health threatglobally. Its pandemic form is caused by strains from a single lineage of the bacterium Vibrio cholerae. The ancestor of this lineageharbored several distinctive characteristics, the most notable being the O1 antigen polysaccharide. This lineage generatedtwo biotypes, first Classical, responsible for six pandemics, and later El Tor, responsible for the seventh and ongoing pandemic.Just as El Tor replaced Classical as the main cause of outbreaks in the last fifty years, several variants of El Tor have evolved anddisplaced their predecessors worldwide. Understanding the ecology, evolution and dispersal of pandemic V. cholerae is centralto studying this complex disease with environmental reservoirs. Here, we present recent advancements of our knowledge on theemergence and spread of the pandemic generating lineage of V. cholerae in the light of established eco-evolutionary observations.Specific ecological interactions shape seasonal cholera, playing a role in the abundance and distribution of its causative agent.Both species-specific and lineage-specific genetic determinants play a role in the ability of V. cholerae strains to cause pandemicswith seasonal outbreaks, having evolved gradually over centuries. On the basis of the current understanding, we outline futurethreats and changes in biogeographical and genomic-based investigation strategies to combat this global problem

FILAMENTOUS BACTERIOPHAGE ASSOCIATED WITH SHAPING COMMUNITY STRUCTURE AND FITNESS OF INVASIVE VIBRIO PARAHAEMOLYTICUS ST36

Vibrio parahaemolyticus a ubiquitous coastal inhabitant, is the leading cause of bacterial seafood-borne illnesses in the United States. An increasing number of reported cases and rapid expansion into new areas has led to the classification of V. parahaemolyticus as an emergent pathogen. Most strains of V. parahaemolyticus are not virulent; however, the spread of virulent lineages from their native ranges to new locations has contributed drastically to the increase in vibriosis attributed to V. parahaemolyticus in recent years. In the United States (US), sequence type (ST) 36, a virulent strain endemic to the Pacific Northwest (PNW), spread from its native range up and down both coasts of North America even crossed the Atlantic to cause an outbreak in Spain in 2012, Specifically, the North Atlantic coast of the US traditionally did not have a major disease burden due to V. parahaemolyticus; however, the introduction of ST36 and the evolution of local pathogenic lineages have led to a sharp increase in the number of cases traced to product from this region. Here we use genomics and phylogeographic analysis to examine the dynamics of the expansion of ST36 and its subsequent establishment in Northeast coastal waters. The impact of basal acquisition of two unique filamentous bacteriophages by distinct clonal clades within the Northeastern ST36 populations is also explored. We propose that the acquisition of these bacteriophages influenced the fitness of their hosts and enabled the establishment of robust local populations of pathogenic V. parahaemolyticus, contributing greatly to the disease burden in the Northeast. Filamentous bacteriophages are distributed throughout many V. parahaemolyticus populations and may be important drivers of evolution amongst these strains. In direct competition under laboratory conditions, the bacteriophage associated with the Gulf of Maine clonal population, Vipa26, does not impact growth of persistently infected isolates and protects them from superinfection by similar phages. Upon new infection, the growth of susceptible isolates slows dramatically before the integration and down regulation of phage production. qPCR assays for integrated and replicative form of phage elucidate this dynamic during infection. This implicates Vipa26 as a potential sword and shield for this strain, possibly aiding the progenitor of the Gulf of Maine population of ST36 in its subsequent global expansion. Impact of phage on biofilm formation, resistance to predatory grazing and competitive fitness in natural seawater microcosms were also investigated. These studies indicate that phage integration is linked to environmental fitness of ST36 and further investigation into the phage-host relationship is warranted to shed light onto the dynamics of the establishment of novel V. parahaemolyticus populations

Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels

Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels’ species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

<p>Abstract</p> <p>Background</p> <p>The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea.</p> <p>Results</p> <p>We have identified <it>in silico </it>the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity.</p> <p>Conclusion</p> <p>This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future structural and evolutionary studies of the cystatin superfamily as well as of other protease inhibitors and proteases.</p

Exploring the genomic and phenotypic diversity of the Vibrio cholerae species

Vibrio cholerae is the aetiological agent of cholera, an acute diarrhoeal disease which is estimated to result in up to 143,000 deaths per annum. Cholera is a considerable public health concern because it can spread rapidly in and explosive pandemics. Current pandemic cholera is caused by a highly-clonal phylogenetic lineage of V. cholerae serogroup O1, which spreads across the globe in periodic ‘waves’. However, V. cholerae is a species rich in diversity, and although much is known about the population structure of the pandemic lineages, the biology and pathogenicity of non-pandemic and non-O1 V. cholerae has been comparatively neglected. In this dissertation, I have studied the biology, genome dynamics, and diversity of non-pandemic V. cholerae, in comparison to the current pandemic lineage. I first present an analysis of the 1992-1998 cholera epidemic in Argentina, a country which had been free of pandemic cholera for nearly 100 years before 1992. I use the genome sequences of 490 V. cholerae from Argentina to study the micro-evolution of the pandemic lineage upon its introduction into a naïve population. I use these data to describe the progression of the Argentinian cholera epidemic using genomic epidemiology approaches, and to contrast this pandemic lineage to the non-epidemic V. cholerae that were present in Argentina at the same time as the pandemic lineage. I then present a study of important recent and historical V. cholerae isolates, sequenced to completion using long-read technologies. I describe aspects of these genomes that could only be resolved using closed assemblies, and present functional validations of several in silico observations. Having performed this forensic, manual study of a small number of genomes, I then extrapolate those insights into a wider context, by mapping the distribution of key genetic determinants of important V. cholerae phenotypes across a phylogenetic tree of 651 highly-diverse V. cholerae. Finally, I integrate the knowledge gained in this research to make a rational selection of V. cholerae isolates for transcriptomic analysis, based on their phylogenetic position and gene content, to investigate whether differential gene expression might explain the stark differences between pandemic and non-pandemic V. cholerae. The data presented here add substantially to our understanding of the diversity of V. cholerae. They emphasise the stark differences in genome flux and evolution between pandemic and non-pandemic lineages. They also show that many of the genetic and phenotypic markers of epidemic and pandemic lineages are misleading, and do not describe that which they were originally chosen to describe.Wellcome (grant 206194) Wellcome Sanger Institute PhD Studentshi

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host-microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host-symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host

Use of Whole Genome Phylogeny and Comparisons in the Development of a Multiplex-PCR Assay to Identify Sequence Type 36 Vibrio parahaemolyticus

Vibrio parahaemolyticus sequence type (ST) 36 strains that are native to the Pacific Ocean have recently caused multi-state outbreaks of gastroenteritis linked to shellfish harvested from the Atlantic Ocean. Whole genome comparisons of 295 genomes of V. parahaemolyticus, including several traced to northeastern US sources, were used to identify diagnostic loci: one putatively encoding an endonuclease (prp), and two others potentially conferring O-antigenic properties (cps and flp). The combination of all three loci was present only in one clade of closely-related strains, of ST36, ST59 and one additional unknown sequence type. However, each locus was also identified outside this clade, with prp and flp occurring in only two non-clade isolates, and cps in four. Based on the distribution of these loci in sequenced genomes, prp could identify clade strains with \u3e99% accuracy, but the addition of one more locus would increase accuracy to 100%. Oligonucleotide primers targeting prp and cps were combined in a multiplex PCR method that defines species using the tlh locus, and determines presence of both the tdh and trh hemolysin-encoding genes which are also present in ST36. Application of the method in vitro to a collection of 94 clinical isolates collected over a four year period in three Northeastern US, and 87 environmental isolates, revealed the prp and cps amplicons were only detected in clinical isolates identified as belonging to the ST36-clade, and in no environmental isolates from the region. The assay should improve detection and surveillance, thereby reducing infections