Fabini Graduates with a PhD!

Fabini, who joined the Boucher lab in September 2012, has successfully defended his PhD thesis, entitled "Taxonomy of bacteria in the genomic era." After publishing 11 authored and co-authored papers (plus 4 more in the pipeline), he is off to be a Postdoc in the labs of Dr. Dominic Sauvageau (Department of Chemical and Materials Engineering) and Dr. Lisa Stein (Department of Biological Sciences) at the University of Alberta. Congrats, Fabini!

It's DOCTOR Paul now!

After almost five years to the day, Paul successfully defended his thesis "Population dynamics of Vibrio cholerae and its close relative Vibrio metoecus in an aquatic ecosystem" and is now just a few thesis edits away from officially becoming a doctor! Paul was Yan's first grad student and is moving on to do a postdoc in the lab of Dr. Howard Ochman at the University of Texas at Austin. For the time being, he will still remain in Edmonton over the summer to wrap up various projects from his Ph.D.

Congrats Paul!

Evolution of the Type VI Secretion System in Vibrio cholerae

Paul and Yan's new paper, "Sequential displacement of type VI secretion system effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae," is out!

In collaboration with Dr. Stefan Pukatzki (University of Colorado Denver), Dr. Daniele Provenzano (University of Texas Rio Grande Valley), and Dr. Daniel Unterweger (University of Oxford), Paul and Yan conducted an extensive study on the role of horizontal gene transfer in shaping the diversity of type VI secretion system (T6SS) loci in V. cholerae and closely related species. They discovered the existence of complex arrays of effector and immunity genes in these loci. These arrays differ even between closely related sympatric strains and appear to be formed by successive horizontal gene transfer events. The resulting accumulation of large numbers of immunity genes potentially enhance the recipient's fitness in T6SS-mediated bactericidal interactions. Additionally, they show how the accumulation of T6SS elements through horizontal gene transfer could have contributed to the evolution of some V. cholerae strains from harmless environmental bacteria to pandemic pathogens.

Whole-genome phylogeny and T6SS effector-immunity module composition of V. cholerae and closely related species (from Kirchberger et al., 2017)

A Genomic Island in Vibrio cholerae with CRISPR-Cas and T6SS Regions

Yan, Fabini, and Paul collaborated with Dr. Maurizio Labbate (University Technology Sydney) and published a paper in Scientific Reports about a ~28-kb genomic island (GI; designated as GIVchS12) in a non-O1/O139 strain of Vibrio cholerae located in the same position where the Vibrio Pathogenicity Island - 1 (VPI-1) would be as it has VPI-1 site-specific recombination characteristics. VPI-1, which has so far only been found in some O1 and O139 V. cholerae strains (with pathogenic strains causing cholera epidemics and pandemics), contains the toxin-coregulated pilus (tcp) cluster. TCP is a precursor for infection of V. cholerae by the CTX phage (that contains the cholera toxin) as it serves as receptor for the phage. It is also important for the colonization of the small intestine during V. cholerae infection of the host. On the other hand, GIVchS12 does not contain the same genes as VPI-1. It contains CRISPR-Cas and type VI secretion system (T6SS) modules. CRISPR-Cas is a defense mechanism by bacteria against unwanted lateral gene transfer by recognizing foreign DNA and cleaving it. T6SS is for inter-cell anatgonism, where T6SS-harbouring bacteria produce a membrane-spanning protein complex used to puncture and kill nearby eukaryotic or prokaryotic cells.

Our survey of representative V. cholerae genomes suggests the presence of genomic islands similar to GIVchS12 containing CRISPR-Cas and T6SS modules from various strains. Natural populations of V. cholerae can serve as reservoir for diverse GIs such as GIVchS12.

Schematic representation of V. cholerae S12 genomic island GIVchS12 (from Labbate et al., 2016)

2016 ISME Meeting - Montréal, Quebec

Yan and Paul (here pictured in the amazing Montréal Convention Centre) safely returned from Quebec, where they attended the 16th International Symposium on Microbial Ecology hosted by the International Society for Microbial Ecology (ISME) on August 21-26, 2016. Yan and Paul presented posters titled "Relatives of Vibrio cholerae pandemic strains can be found in non-endemic areas using a novel culture-independent method" and "Mosaic evolution of the Vibrio cholerae Type VI secretion system," respectively. Both posters are projects of Paul, who has clearly been very busy.

At the beautiful Palais des congrès de Montréal

Tania is Back in Bangladesh for More Field Work

From June 29 to August 15, 2016, Tania worked in Dr. Munirul Alam's lab in the International Centre for Diarrhoeal Disease Research, Bangladesh. They worked on a collaborative project, "Genetic tracking and characterization of naturally occurring Vibrio cholerae causing endemic cholera in Bangladesh." There, she helped organize the last rounds of sampling of environmental water to isolate V. cholerae from eight different sites around Dhaka City.

Vibrio cidicii, a Novel Vibrio Species Closely Related to Vibrio navarrensis

The official species description paper of the novel Vibrio species, Vibrio cidicii, is now out. The paper is entitled "Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis" and published in the International Journal of Systematic and Evolutionary Microbiology. Vibrio cidicii was initially identified by the group of Dr. Cheryl Tarr from the Centers for Disease Control and Prevention (CDC) while studying clinical isolates of V. navarrensis. Thus, the new species was named after the CDC.

Characterization of the isolates involved extensive biochemical and genotypic tests, including whole-genome comparisons with close relatives, V. navarrensis and Vibrio vulnificus. Metabolic profiling found one major phenotypic difference between V. cidicii from its closest relatives, the utilization of L-rhamnose, where the V. cidicii isolates are able to utilize the substrate. Genome comparisons and multilocus sequence analysis (MLSA) show that the V. cidicii genomes to belong to a species different from V. navarrensis and V. vulnificus.

This work was in collaboration with the teams of Dr. Cheryl Tarr (CDC), Dr. I. King Jordan (Georgia Institute of Technology), and Dr. Rebecca Case (Department of Biological Sciences). This is the second novel Vibrio species characterized from the Boucher Lab (Vibrio metoecus being the first one).

MLSA of housekeeping genes show distinct clustering of V. cidicii from its closest relatives (from Orata et al., 2016)

Genome Sequences of Bacteria in Close Association with Emiliania huxleyi

Yan and Fabini, in collaboration with the lab of Dr. Rebecca Case (also from the Department of Biological Sciences), released two Genome Announcements today on the genome sequences of bacterial strains isolated from the polymicrobial cultures of coccolith-bearing and naked (no coccolith) microalga Emiliania huxleyi. The Case Lab isolated multiple bacteria from these cultures, including strains of Balneola sp., Erythrobacter sp., Jannaschia sp., Marinobacter sp., Roseovarius sp., and Sulfitobacter spp. among others, which form a symbiotic relationship with E. huxleyi. The Boucher Lab sequenced the genomes of these isolates. This is part of an ongoing work with both labs. We are currently working on resolving the taxonomic inconsistencies within the Rhodobacteraceae family, specifically within the Rosobeacter clade, by comparative genomic analysis.