Concepts in Evolutionary Studies Workshop – Roscoff, France

Biological network analyses have been recently shown to be a powerful tool in biological sciences, playing a crucial role in identifying such processes as horizontal gene transfer and biogeographic patterns. A five day workshop entitled Introduction the concepts and methods of networks in evolutionary studies ran from June 24-30, 2018 in Roscoff, France. The workshop featured leading mathematicians, computer scientists, and both eukaryotic and prokaryotic biologists to offer a comprehensive introduction to concepts of biological networks with a beautiful seaside view.

Kevin attended this workshop last month where he learned how to combine simple python scripts with cutting edge bioinformatics pipeline to construct and analyze different kinds of biological networks. It is anticipated that network analysis will be an important part of his current research project in characterizing the biogeographic distribution of known Vibrio cholerae strains and reconstructing the evolutionary history of the 7th pandemic lineage.

Kevin enjoying the scenic seaside along with the other 2018 workshop members. 

Kevin enjoying the scenic seaside along with the other 2018 workshop members. 

Metagenomics Workshop – Calgary, Alberta

Tareq has just returned from a Genome-centric Metagenomics Workshop hosted by the University of Calgary entitled From community DNA to provisional whole genomes of microbial populations. The workshop consisted of two sessions, with the first part (June 20-22, 2018) with a hands-on approach to generate and prep metagenomic libraries, and the following session (June 25-29, 2018) allowed participants to process the raw dataset into meaningful results.

The workshop was developed by the University of Calgary Energy Bioengineering and Geomicrobiology Research Group.  

A group photo of the attendees at the 2018 Metagenomics Workshop hosted at the University of Calgary in Calgary, Alberta. 

A group photo of the attendees at the 2018 Metagenomics Workshop hosted at the University of Calgary in Calgary, Alberta. 

2018 CIFAR-IMB General Meeting – Banff, Alberta

Banff, Alberta marks the final location for the last annual Integrated Microbial Biodiversity (IMB) meeting hosted by the Canadian Institute for Advanced Research (CIFAR). CIFAR fellows were invited to attend the meeting along with a post-doc or graduate student in their lab as a trainee. The conference was held from June 12-15, 2018, with a trainee workshop hosted on June 11 to help participants assess various career paths within, and outside of, academia. The meeting had intriguing research and interesting talks and discussion from a wide variety of microbial backgrounds. 

Yan attended the conference alongside Nora, who presented a poster of her ongoing research entitled "Type VI secretion system effector immunity diversity in intra-location Vibrio cholerae populations".  Yan and Nora also unveiled a fun, interactive type VI secretion card game during the meeting that was warmly received by members.

The final IMB meeting finished with prominent scientists from around the world sharing inspiring, cutting edge ideas. Collaboration between members and pioneering research will continue, allowing a greater understanding of the microbial world around us.  

Nora behind her research during the poster presentations. 

Nora behind her research during the poster presentations. 

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!

Tracking the Pandemic Generating Lineage of Vibrio cholerae

In collaboration with Dr. Munirul Alam (International Centre for Diarrheal Disease Research, Bangladesh), Yan and Tareq's new review outlining the evolution and dissemination of the pandemic lineage of Vibrio cholerae has been published. "Emergence, ecology and dispersal of the pandemic generating Vibrio cholerae lineage" is now available in the open access journal of International Microbiology.

The initial development of pandemic Vibrio cholerae highlights important gene acquisition events required for the Pandemic Generating (PG) lineage to form before being able to infect human hosts. These preliminary gene acquisition stages drive the evolution of pandemic cholera, up to the seventh and current pandemic El Tor strains. Phylogenetic analysis of PG strains indicate a replacement of El Tor predecessors that is now associated with current cholera outbreaks. Pandemic V. cholerae exists in two life stages, as a pathogen in human hosts and in environmental reservoirs, with ecological factors influencing regions that have annual patterns of infection outbreaks, such as water chemistry and host associations in environmental reservoirs. This review provides insight into the evolutionary path of PG V. cholerae, and its dispersal in the environment outside of human hosts. 

Phylogenetic analysis of pandemic  V. cholerae  evolution (from   Islam et al., 2017  )

Phylogenetic analysis of pandemic V. cholerae evolution (from Islam et al., 2017)

Welcome Kevin and Nora!

Kevin Liang and Nora Hussain have been officially welcomed into the Boucher lab as Masters students! Kevin has a B.Sc. in Bioinformatics from the University of Alberta, and Nora graduated from the University of Alberta with a B.Sc. with a specialization in Microbiology. Both Kevin and Nora started off doing undergraduate research projects in the Boucher lab, and continued on to pursue graduate studies after completing their B.Sc. degrees. This will be the first group of Masters students in the Boucher lab.  

Welcome back, Kevin and Nora!


Kevin and Nora are the newest graduate recruits in the Boucher lab. 

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)