Population Structure of Single-Source Vibrio cholerae

Our lab's newest paper is finally out! Bacteria display a stunning array of diversity, from higher order groups all the way down to the subspecies level of endlessly differing strains. Our main organism of study, Vibrio cholerae, is no different. Only by deeply sampling groups of closely related organisms from the same environment can we begin to understand how this diversity arises – both for V. cholerae and bacteria in general. Using multi locus sequence typing and phylogenomics, we found that the scenic Oyster Pond and Lagoon ecosystem in Woods Hole, Massachusetts is dominated by a handful of distantly related V. cholerae strains, with many more found in much lower numbers, perhaps waiting for the right opportunity to rise to the top. The dominating strains show signs of ecological differentiation, but are likely in strong competition with each other, as evidenced by their different repertoires of type VI secretion system effectors that mediate fatal bacterial interactions. Oh, and some are bioluminescent!

The paper is entitled "A small number of phylogenetically distinct clonal complexes dominate a coastal Vibrio cholerae population" and published in Applied and Environmental Microbiology. The work is a carryover from Yan's postdoc at the Massachusetts Institute of Technology (as evidenced by having Dr. Kathryn Kauffman and Dr. Martin Polz from MIT as co-authors), so it has been a long time in the making!

Clonal backbone of V. cholerae sampled from different locations around Oyster Pond (from Kirchberger et al., 2016)

2016 CIFAR-IMB General Meeting – Toronto, Ontario

The Integrated Microbial Biodiversity (IMB) Program of the Canadian Institute for Advanced Research (CIFAR) held its annual conference for members (and their students) at the Intercontinental Hotel, Toronto, Ontario on June 1-4, 2016. The conference was remarkable, with amazing talks from distinguished scientists from different parts of the world, lively scientific discussions, and sharing of innovative ideas.

Yan was accompanied by Tareq this year. Yan gave a talk entitled "Relatives of Vibrio cholerae pandemic strains can be found in non-endemic areas using a novel culture-independent method," and Tareq presented a poster of his current work entitled "The elusive descendants of the pandemic Vibrio cholerae ancestor: a diverse and dangerous bunch."

Toronto skyline

Commentary on the Local Diversity of Vibrio cholerae in Mexico

Yan's commentary article entitled "Sustained local diversity of Vibrio cholerae O1 biotypes in a previously cholera-free country," is now available in mBio. This commentary is for a recently published study by Dr. Seon Young Choi and colleagues (University of Maryland), also in mBio, on three decades of V. cholerae monitoring from environmental and clinical sources in Mexico. This long-term effort surprisingly found a large number of non-toxigenic V. cholerae strains that are very closely related to the pandemic agents of cholera. Yan speculates that these strains could serve as progenitors for novel toxigenic lineages through horizontal gene transfer in environmental reservoirs. He suggests that widespread and large environmental sampling efforts are needed to detect the presence of these elusive strains, which, incidentally, is exactly what his lab is doing!

Phylogenetic relationships of pandemic V. cholerae strains and their relatives (from Boucher, 2016)

Temporal Distribution of Vibrio parahaemolyticus in the Bay of Bengal, Bangladesh

Yan and his colleagues published a paper, "Major tdh+ Vibrio parahaemolyticus serotype changes temporally in the Bay of Bengal estuary of Bangladesh," today in the journal Infection, Genetics, and Evolution. This work was done in collaboration with Dr. Munirul Alam, senior author of the paper, from the International Centre for Diarrhoeal Disease Research, Bangladesh, as well as colleagues from the University of Dhaka and the National Institute of Infectious Diseases, Japan. Vibrio parahaemolyticus causes seafood-related gastroenteritis and shows a temporal serotypic shift from predominantly non-pandemic serotypes in 2006-2007 to predominantly pandemic serotypes in 2008, underscoring the need for routine environmental monitoring to prevent V. parahaemolyticus-related diseases.

VIBRIO2016 Conference – Roscoff, France

Greetings from Roscoff!

The VIBRIO2016 Conference concluded today. This conference is the biggest gathering of scientists with one thing in common – their love for vibrios. Current researches on Vibrio cholerae, Vibrio vulnificus, Vibrio fischeri, and other vibrios were presented. Great French wine and Vibrio-free seafood were also very abundant at the conference.

Yan presented a talk about work in the lab on the population structure of natural populations of V. cholerae. Fabini's poster presentation was on a newly characterized Vibrio species, Vibrio cidicii, work he and Yan did with collaborators from the University of Alberta, Georgia Institute of Technology, and the Centers for Disease Control and Prevention (CDC... cidicii. Get it?).

The conference was organized by Dr. Frédérique Le Roux and her lab team from the Station Biologique Roscoff. VIBRIO2017 will (possibly) be held in Chicago, USA.

Vibrio2016 attendees

Computational Microbial Ecology Workshop – Romulus, Michigan

Fabini attended the Computational Microbial Ecology Workshop in Romulus, Michigan on November 2-4, 2015, hosted by Dr. Patrick Schloss of the University of Michigan. The workshop was geared towards people with interests in microbial ecology that would like to learn computer programming using the R language. It involved a blend of lecture/discussion and hands-on use of R with real data.

Learning R programming with Dr. Patrick Schloss

Of Dense Populations and Vibrio cholerae Evolution

Yan and Fabini published a hypothesis paper entitled "The out-of-the-delta hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen" in Frontiers in Microbiology. Dr. Munirul Alam, a collaborator from the International Centre for Diarrhoeal Disease Research, Bangladesh, is also co-author of the paper.

The authors propose that the unique human and physical geography of the Ganges Delta caused the naturally-occurring and nonpathogenic Vibrio cholerae to evolve into a deadly human pathogen. This is mainly due to the regular ingestion of V. cholerae through consumption of brackish water by the inhabitants of the Ganges Delta area and the subsequent release of V. cholerae back into the environment, therefore creating a continuous selection pressure for V. cholerae to adapt to life in the human gut.

The red and blue areas on the world map each house 5% of the world's population (from Boucher et al., 2015; map constructed by Max Galka, used with permission)

Genetic Interactions Between Vibrio metoecus and Vibrio cholerae

Members of the Boucher Lab recently published a paper, "The dynamics of genetic interactions between Vibrio metoecus and Vibrio cholerae, two close relatives co-occurring in the environment," in Genome Biology and Evolution. The known closest relative of V. cholerae is V. metoecus. The paper discusses the extent of gene exchange by horizontal gene transfer between the two species, suggesting that there is a strong bias in the direction of gene transfer from the former to the latter.

Yan, Fabini, and Paul are joined by Dr. Cheryl Tarr (Centers of Disease Control and Prevention), Raphaël Méheust (Université Pierre et Marie Curie), and Jed Barlow (Department of Computing Science) as co-authors. Jed is a former undergraduate student of the lab.

Whole genome BLAST atlas of various V. cholerae (Vc) and V. metoecus (Vm) strains (from Orata et al., 2015)

Celebratory Barbecue!

To celebrate lab members passing their candidacy exams and to welcome the new graduate students, Yan and Rebecca hosted a joint Boucher-Case lab barbecue party. Friends and family joined to celebrate as well.

Paul, Fabini, Tania, and Anna (of the Case Lab) are now official Ph.D. candidates after recently passing their candidacy exams. Tareq is the new Ph.D. student of the Boucher Lab. For the Case Lab, Yue just started his M.Sc. this month, and Albert will commence his Ph.D. in January.

Lab party!