Publications by authors named "Fabini D Orata"

18 Publications

  • Page 1 of 1

Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) Is Essential for Growth of the Methanotroph Methylococcus capsulatus Strain Bath.

Appl Environ Microbiol 2021 08 26;87(18):e0088121. Epub 2021 Aug 26.

Biosciences Center, National Renewable Energy Laboratorygrid.419357.d, Golden, Colorado, USA.

The ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzyme found in plants, algae, and an array of autotrophic bacteria is also encoded by a subset of methanotrophs, but its role in these microbes has largely remained elusive. In this study, we showed that CO was requisite for RubisCO-encoding Methylococcus capsulatus strain Bath growth in a bioreactor with continuous influent and effluent gas flow. RNA sequencing identified active transcription of several carboxylating enzymes, including key enzymes of the Calvin and serine cycles, that could mediate CO assimilation during cultivation with both CH and CO as carbon sources. Marker exchange mutagenesis of M. capsulatus Bath genes encoding key enzymes of potential CO-assimilating metabolic pathways indicated that a complete serine cycle is not required, whereas RubisCO is essential for growth of this bacterium. CO tracer analysis showed that CH and CO enter overlapping anaplerotic pathways and implicated RubisCO as the primary enzyme mediating CO assimilation in Bath. Notably, we quantified the relative abundance of 3-phosphoglycerate and ribulose-1,5-bisphosphate C isotopes, which supported that RubisCO-produced 3-phosphoglycerate is primarily converted to ribulose-1-5-bisphosphate via the oxidative pentose phosphate pathway in Bath. Collectively, our data establish that RubisCO and CO play essential roles in Bath metabolism. This study expands the known capacity of methanotrophs to fix CO via RubisCO, which may play a more pivotal role in the Earth's biogeochemical carbon cycling and greenhouse gas regulation than previously recognized. Further, Bath and other CO-assimilating methanotrophs represent excellent candidates for use in the bioconversion of biogas waste streams that consist of both CH and CO. The importance of RubisCO and CO in Bath metabolism is unclear. In this study, we demonstrated that both CO and RubisCO are essential for Bath growth. CO tracing experiments supported that RubisCO mediates CO fixation and that a noncanonical Calvin cycle is active in this organism. Our study provides insights into the expanding knowledge of methanotroph metabolism and implicates dually CH/CO-utilizing bacteria as more important players in the biogeochemical carbon cycle than previously appreciated. In addition, and other methanotrophs with CO assimilation capacity represent candidate organisms for the development of biotechnologies to mitigate the two most abundant greenhouse gases, CH and CO.
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http://dx.doi.org/10.1128/AEM.00881-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388818PMC
August 2021

Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, fam. nov.

Front Microbiol 2021 25;12:683109. Epub 2021 Jun 25.

Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.

The family consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the family. Representatives of the roseobacter clade not only have different environmental adaptions from other isolates but were also found to be distinct based on genomic, phylogenetic, and -predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
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http://dx.doi.org/10.3389/fmicb.2021.683109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267831PMC
June 2021

Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species ( sp. nov.) with a History of Association with Humans.

Appl Environ Microbiol 2021 08 11;87(17):e0042221. Epub 2021 Aug 11.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.

Most efforts to understand the biology of Vibrio cholerae have focused on a single group, the pandemic-generating lineage harboring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in the V. cholerae populations inhabiting regions with a history of cholera cases and those lacking such a history, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka, Bangladesh (where cholera is endemic), located in the Ganges Delta, and those in Falmouth, MA (no known history of cholera), a small coastal town on the United States east coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka, which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny for the V. cholerae species and were sufficiently differentiated genetically and phenotypically to form a novel species. A retrospective search revealed that strains from this species have been anecdotally found from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhea. In 1935, Gardner and Venkatraman unofficially referred to a member of this group as Vibrio paracholerae. In recognition of this earlier designation, we propose the name sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species. Cholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution, and environmental adaptation of the causative agent (Vibrio cholerae) and tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics of Vibrio cholerae in an inland locality, which is known as endemic for cholera, and compared them with those of a cholera-free coastal location. We found the consistent presence of the pandemic-generating lineage of V. cholerae in Dhaka, where cholera is endemic, and an exclusive presence of a lineage phylogenetically distinct from other V. cholerae lineages. Our study suggests that this lineage represents a novel species that has pathogenic potential and a human link to its environmental abundance. The possible association with human populations and coexistence and interaction with toxigenic V. cholerae in the natural environment make this potential human pathogen an important subject for future studies.
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http://dx.doi.org/10.1128/AEM.00422-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357300PMC
August 2021

Simultaneous Quantification of and with Its O1 Serogroup and Toxigenic Subpopulations in Environmental Reservoirs.

Pathogens 2020 Dec 16;9(12). Epub 2020 Dec 16.

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

is a recently described aquatic bacterium and opportunistic pathogen, closely related to and often coexisting with To study the relative abundance and population dynamics of both species in aquatic environments of cholera-endemic and cholera-free regions, we developed a multiplex qPCR assay allowing simultaneous quantification of total and (including toxigenic and O1 serogroup) cells. The presence of was restricted to samples from regions that are not endemic for cholera, where it was found at 20% of the abundance of . In this environment, non-toxigenic O1 serogroup represents almost one-fifth of the total population. In contrast, toxigenic O1 serogroup was also present in low abundance on the coast of cholera-endemic regions, but sustained in relatively high proportions throughout the year in inland waters. The majority of cells from both species were recovered from particles rather than free-living, indicating a potential preference for attached versus planktonic lifestyles. This research further elucidates the population dynamics underpinning and its closest relative in cholera-endemic and non-endemic regions through culture-independent quantification from environmental samples.
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http://dx.doi.org/10.3390/pathogens9121053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766680PMC
December 2020

A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera.

J Bacteriol 2020 11 19;202(24). Epub 2020 Nov 19.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for , a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). Toxigenic isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
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http://dx.doi.org/10.1128/JB.00086-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685551PMC
November 2020

Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population.

Environ Microbiol 2020 10 6;22(10):4244-4256. Epub 2020 Feb 6.

Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.

Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating lineage capable of causing the diarrhoeal disease cholera. Assessing the composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively. We developed a culture-independent amplicon sequencing strategy based on the protein-coding gene viuB (vibriobactin utilization) to study the structure of a V. cholerae population over the course of a summer. We show that the 26 co-occurring V. cholerae lineages continuously compete for limited space on nutrient-rich particles where only a few of them can grow to large numbers. Differential abundance of lineages between locations and size-fractions associated with a particle-attached or free-swimming lifestyle could reflect adaptation to various environmental niches. In particular, a major V. cholerae lineage occasionally grows to large numbers on particles but remain undetectable using isolation-based methods, indicating selective culturability for some members of the species. We thus demonstrate that isolation-based studies may not accurately reflect the structure and complex dynamics of V. cholerae populations and provide a scalable high-throughput method for both epidemiological and ecological approaches to studying this species.
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http://dx.doi.org/10.1111/1462-2920.14921DOI Listing
October 2020

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order ) Calls for the Reclassification of Members at the Genus and Species Levels.

Front Microbiol 2018 19;9:3162. Epub 2018 Dec 19.

Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.

The order constitutes the methanotrophs - bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons - average amino acid identity, digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) - were performed on 91 genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus , , "," , , and are reclassified to a newly proposed genus, gen. nov.; they are therefore renamed to comb. nov., "" comb. nov., comb. nov., comb. nov., and comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of with and , the reclassification of the former species to comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), is proposed to be a later heterotypic synonym of (89% dDDH and 99% ANI). Also, the effectively but not validly published "" was identified as (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as , each represent a putative novel species of the genus (21-35% dDDH and 74-88% ANI against ) and were reclassified as sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.
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http://dx.doi.org/10.3389/fmicb.2018.03162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315193PMC
December 2018

Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification.

Genome Announc 2018 Apr 26;6(17). Epub 2018 Apr 26.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

strain FJG1 is a member of the gammaproteobacterial methanotrophs. The sequenced genome of FJG1 reveals the presence of genes that encode methane, methanol, formaldehyde, and formate oxidation. It also contains genes that encode enzymes for nitrate reduction to nitrous oxide, consistent with the ability of FJG1 to couple denitrification with methane oxidation.
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http://dx.doi.org/10.1128/genomeA.00276-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920175PMC
April 2018

Bacillus amyloliquefaciens ssp. plantarum F11 isolated from Algerian salty lake as a source of biosurfactants and bioactive lipopeptides.

FEMS Microbiol Lett 2018 01;365(1)

Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada.

In this study, we identified a new Bacillus strain isolated from an Algerian salty lake that produces metabolites that are active against Gram-positive and Gram-negative bacteria, as well as fungal pathogens. The draft genome sequence of the strain is presented herein. Genome sequence analysis identified the strain to be B. amyloliquefaciens subspecies plantarum F11, and showed that the strain carries the gene clusters for the production of a number of bioactive and surface-active compounds. These include the lipopeptides surfactin and fengycin, antibacterial polyketides macrolactin and bacillaene, and a putative novel lanthipeptide, among others. Through an activity-guided purification method using hydrophobic interaction chromatographic techniques, we confirmed the ability of the strain to produce fengycin lipopeptides. The identities of the isolated fengycin homologs were ascertained through tandem mass spectrometry.
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http://dx.doi.org/10.1093/femsle/fnx248DOI Listing
January 2018

Complete Genome Sequence of sp. Strain 2521-89, a Close Relative of Isolated from Lake Water in New Mexico, USA.

Genome Announc 2017 Aug 31;5(35). Epub 2017 Aug 31.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

sp. strain 2521-89 is an environmental isolate from lake water in New Mexico, USA. Average nucleotide identity, DNA-DNA hybridization, and core genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis suggest that this may be a potentially novel species that is closely related to .
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http://dx.doi.org/10.1128/genomeA.00905-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578854PMC
August 2017

A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules.

Sci Rep 2016 11 15;6:36891. Epub 2016 Nov 15.

University of Technology Sydney, The ithree institute, Sydney, 2007, Australia.

Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139 Vibrio cholerae. Mobile genetic elements such as genomic islands (GIs) have been pivotal in the evolution of O1/O139 V. cholerae. Perhaps the most important GI involved in cholera disease is the V. cholerae pathogenicity island 1 (VPI-1). This GI contains the toxin-coregulated pilus (TCP) gene cluster that is necessary for colonization of the human intestine as well as being the receptor for infection by the cholera-toxin bearing CTX phage. In this study, we report a GI (designated GIVchS12) from a non-O1/O139 strain of V. cholerae that is present in the same chromosomal location as VPI-1, contains an integrase gene with 94% nucleotide and 100% protein identity to the VPI-1 integrase, and attachment (att) sites 100% identical to those found in VPI-1. However, instead of TCP and the other accessory genes present in VPI-1, GIVchS12 contains a CRISPR-Cas element and a type VI secretion system (T6SS). GIs similar to GIVchS12 were identified in other V. cholerae genomes, also containing CRISPR-Cas elements and/or T6SS's. This study highlights the diversity of GIs circulating in natural V. cholerae populations and identifies GIs with VPI-1 recombination characteristics as a propagator of CRISPR-Cas and T6SS modules.
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http://dx.doi.org/10.1038/srep36891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109276PMC
November 2016

Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis.

Int J Syst Evol Microbiol 2016 Oct 27;66(10):4148-4155. Epub 2016 Jul 27.

Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus, based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis, their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA-DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4-95.8 % and 61.9-64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus. Based on these differences, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.
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http://dx.doi.org/10.1099/ijsem.0.001327DOI Listing
October 2016

Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516.

Genome Announc 2016 Jul 14;4(4). Epub 2016 Jul 14.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

Strains of Sulfitobacter spp., Erythrobacter sp., and Marinobacter sp. were isolated from a polymicrobial culture of the naked (N-type) haptophyte Emiliania huxleyi strain CCMP1516. The genomes encode genes for the production of phytohormones, vitamins, and the consumption of their hosts' metabolic by-products, suggesting symbiotic interactions within this polymicrobial culture.
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http://dx.doi.org/10.1128/genomeA.00674-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945806PMC
July 2016

Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217.

Genome Announc 2016 Jul 14;4(4). Epub 2016 Jul 14.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

Strains of Rhodobacteraceae, Sphingomonadales, Alteromonadales, and Bacteroidetes were isolated from a polymicrobial culture of the coccolith-forming (C-type) haptophyte Emiliania huxleyi strain M217. The genomes encode genes for the production of algal growth factors and the consumption of their hosts' metabolic by-products, suggesting that the polymicrobial culture harbors many symbiotic interactions.
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http://dx.doi.org/10.1128/genomeA.00673-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945805PMC
July 2016

A Small Number of Phylogenetically Distinct Clonal Complexes Dominate a Coastal Vibrio cholerae Population.

Appl Environ Microbiol 2016 09 30;82(18):5576-86. Epub 2016 Aug 30.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

Unlabelled: Vibrio cholerae is a ubiquitous aquatic microbe in temperate and tropical coastal areas. It is a diverse species, with many isolates that are harmless to humans, while others are highly pathogenic. Most notable among them are strains belonging to the pandemic O1/O139 serogroup lineage, which contains the causative agents of cholera. The environmental selective regimes that led to this diversity are key to understanding how pathogens evolve in environmental reservoirs. A local population of V. cholerae and its close relative Vibrio metoecus from a coastal pond and lagoon system was extensively sampled during two consecutive months across four size fractions (480 isolates). In stark contrast to previous studies, the observed population was highly clonal, with 60% of V. cholerae isolates falling into one of five clonal complexes, which varied in abundance in the short temporal scale sampled. V. cholerae clonal complexes had significantly different distributions across size fractions and the two environments sampled, the pond and the lagoon. Sequencing the genomes of 20 isolates representing these five V. cholerae clonal complexes revealed different evolutionary trajectories, with considerable variations in gene content with potential ecological significance. Showing genotypic differentiation and differential spatial distribution, the dominant clonal complexes are likely ecologically divergent. Temporal variation in the relative abundance of these complexes suggests that transient blooms of specific clones could dominate local diversity.

Importance: Vibrio cholerae is commonly found in coastal areas worldwide, with only a single group of this bacterium capable of causing severe cholera outbreaks. However, the potential to evolve the ability to cause disease exists in many strains of this species in its aquatic reservoir. Understanding how pathogenic bacteria evolve requires the study of their natural environments. By extensive sampling in a geographically restricted location in the United States, we found that most cells of a V. cholerae population belong to only a small number of strains. Analysis of their genome composition and spatial distribution indicates differential environmental adaptations between these strains. Other strains exist in smaller numbers, and the population was found to be temporally varied. This suggests frequent bloom and collapse cycles on a time scale of weeks. These population dynamics make it possible that more virulent strains could stochastically rise to large numbers, allowing for infection to occur.
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http://dx.doi.org/10.1128/AEM.01177-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007767PMC
September 2016

The out-of-the-delta hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen.

Front Microbiol 2015 19;6:1120. Epub 2015 Oct 19.

Centre for Communicable Diseases, International Centre for Diarrhoeal Disease Research , Bangladesh (ICDDR,B), Dhaka, Bangladesh.

Cholera is a diarrheal disease that has changed the history of mankind, devastating the world with seven pandemics from 1817 to the present day. Although there is little doubt in the causative agent of these pandemics being Vibrio cholerae of the O1 serogroup, where, when, and how this pathogen emerged is not well understood. V. cholerae is a ubiquitous coastal species that likely existed for tens of thousands of years. However, the evolution of a strain capable of causing a large-scale epidemic is likely more recent historically. Here, we propose that the unique human and physical geography of low-lying river deltas made it possible for an environmental bacterium to evolve into a deadly human pathogen. Such areas are often densely populated and salt intrusion in drinking water frequent. As V. cholerae is most abundant in brackish water, its favored environment, it is likely that coastal inhabitants would regularly ingest the bacterium and release it back in the environment. This creates a continuous selection pressure for V. cholerae to adapt to life in the human gut.
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http://dx.doi.org/10.3389/fmicb.2015.01120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609888PMC
November 2015

The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.

Genome Biol Evol 2015 Oct 9;7(10):2941-54. Epub 2015 Oct 9.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada

Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
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http://dx.doi.org/10.1093/gbe/evv193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684700PMC
October 2015

The 2010 cholera outbreak in Haiti: how science solved a controversy.

PLoS Pathog 2014 Apr 3;10(4):e1003967. Epub 2014 Apr 3.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.

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http://dx.doi.org/10.1371/journal.ppat.1003967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974815PMC
April 2014
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