New Vibrio cholerae Core-Genome Multi-Locus Sequence Typing (cgMLST) Website Online

            A novel core-genome Multi-Locus Sequence Typing (cgMLST) scheme for V. cholerae is now publicly available on pubmlst.org/vcholerae. New genomes can now be submitted and analyzed on PubMLST within minutes. Tools such as GrapeTree (Zhou et al 2018), iTOL (Letunic et al 2006), and PHYLOViZ (Francisco et al 2012) are all integrated within the website to allow for quick follow-up analyses. This cgMLST scheme, containing 2443 core genes, has been used to analyze over 1000 V. cholerae genomes from both private collections and publicly available databases. This dataset includes representative isolates from known outbreaks and endemic countries. Along with epidemiological data, it is possible to use this cgMLST scheme to monitor V. cholerae diversity at both the local and global level. 1-1 mapping with a previously established V. cholerae MLST scheme from our lab (Kirchberger et al 2016) has been carried out to allow for backwards compatibility with prior studies. The full manuscript is in preparation which will detail the application of this cgMLST scheme to study cholera outbreaks and its diversity.

Eight Novel Vibrio Genomes Announced

In addition to the nine Vibrio sp. genomes deposited late last November, a new genome announcement with eight additional Vibrio isolates has come out today. Working alongside the US Centers for Disease Control and Prevention again, these newly described Vibrio strains have come from a variety of blood, stool or wound infections, in addition to a previously described environmental strain. All genomes within the article “Draft Genome Sequences of Eight Vibrio sp. Clinical Isolates from across the United States That Form a Basal Sister Clade to Vibrio cholerae” cluster within a single clade, and molecular analyses for species delineation place these isolates at or below the species cutoff values when compared to representative V. cholerae strains. This suggests these strains may form a basal V. cholerae lineage, or a new species related to V. cholerae.

Nine Divergent Vibrio Genomes Announced

The Boucher Lab and the Centres for Disease Control and Prevention in the US have deposited the whole-genomes of nine Vibrio species suggested to belong to a unique basal lineage of Vibrio cholerae, or a new closely related novel species to V. cholerae. The genome report, “Draft Genome Sequences of Nine Vibrio sp. Isolates from across the United States Closely Related to Vibrio cholerae” was published in Microbiology Resource Announcements today. These new genomes, based on molecular analyses, are at the cusp of the delineating species cutoffs.

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!

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