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.

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)

Origin of Lignin Biosynthesis

A new paper, "Ancient origin of the biosynthesis of lignin precursors," was published today in Biology Direct, with Ph.D. student Leen Labeeuw and Dr. Rebecca Case (Department of Biological Sciences) as lead and senior authors, respectively. The authors propose that the genes associated with the biosynthesis of p-coumaryl alcohol, the simplest lignin monomer, found in algal genomes likely evolved long before the transition of photosynthetic eukaryotes to land.

As co-authors, Yan contributed his expertise in phylogenetic analysis and was involved in the design of the experiment, and Dr. Patrick Martone (University of British Columbia) provided novel gene sequences for the study.

Major evolutionary events hypothesized in the evolution of the lignin biosynthetic pathway across the eukaryotic tree (from Labeeuw et al., 2015)

New Vibrio Species Closely Related to Vibrio cholerae

After a long and frustrating debate on what to name the new bacterium, the official species description for Vibrio metoecus is finally published! The paper is entitled "Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens" and published in the International Journal of Systematic and Evolutionary Microbiology today. Yan and Paul lead the research group, which included prominent environmental microbiologist Dr. Rita Colwell (University of Maryland). As the title of the paper mentions, the newly described species, V. metoecus, is now the known closest relative of the well-known V. cholerae.

V. metoecus was formerly and unofficially named V. metecus. The Boucher Lab is currently pursuing more research work to gain insight on the evolution and emergence of this new species.

Electron micrographs of V. metoecus. (A) Scanning electron microscopy, scale bar = 2 μm; (B) Transmission electron microscopy, scale bar = 0.2 μm (from Kirchberger et al., 2014)

Publication Awards for the Boucher Lab

Yan, Fabini, and co-authors, lead by Dr. Lee Katz and Dr. Cheryl Tarr of the Centers for Disease Control and Prevention (CDC), received two prestigious CDC awards in recognition of their paper entitled "Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti," published in the journal mBio on July 2, 2013.

For their work, the group received the James H. Nakano Citation Award from the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) for one of the best papers of 2013 and a Charles C. Shepard Award nomination (Laboratory Science category) from the Agency for Toxic Substances and Disease Registry.

The awards were accepted by members of the CDC group during the ceremony (pictured below).

Accepting the James H. Nakano Citation Award at the CDC (from left): Nakano's son, Lori Gladney, Lee Katz, Cheryl Tarr, Beth Bell (director of NCEZID), Maryann Turnsek, and Molly Freeman (photo by Lee Katz)

Determining the Origin of the 2010 Cholera Outbreak in Haiti

The review article "The 2010 cholera outbreak in Haiti: how science solved a controversy" is now published as part of the PLOS Pathogens Pearls collection. Yan and Fabini are joined by world-renowned scientist Dr. Paul Keim (Northern Arizona University) as co-author. The use of whole-genome sequencing to determine the origin of cholera in Haiti is discussed in the paper.

The article was written specifically for PLOS Pathogens Pearls by invitation from Pearls Editor Dr. Joseph Heitman (Duke University School of Medicine).

Update 1 (April 6, 2014)
The article is featured on the Scientific American Blog Network: "The pathogen detectives: sourcing the post-earthquake cholera outbreak in Haiti" by S.E. Gould.

Update 2 (April 24, 2014)
The article is featured on Nature's Research Highlights – Social Selection, based on popular articles on social media.

How the Haiti cholera outbreak started (from Orata et al., 2014)

Evolutionary Dynamics of the Haitian Cholera Outbreak Strains

Yan and Fabini were part of a huge collaborative group, lead by Dr. Lee Katz and Dr. Cheryl Tarr of the Centers for Disease Control and Prevention (CDC), that published an article today in mBio entitled "Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti." The article shows that the source of cholera, caused by V. cholerae, that hit Haiti in 2010 following the devastating earthquake came from a single source and was not introduced repeatedly to Haiti.

Other members of the group were researchers and public health officials from the National Microbiology Laboratory – Public Health Agency of Canada, Mount Sinai School of Medicine, Georgia Institute of Technology, Pacific Biosciences, Haiti National Public Health Laboratory, and Harvard University.

The manuscript was received, accepted (unconditionally), and published all within SIX WEEKS. The release was also picked up by science news blogs EurekAlert! and mBiosphere.

The radiation of numerous lineages of V. cholerae O1 strains from a single sequence type that predominated in the early part of the Haiti cholera epidemic (from Katz et al., 2013)

Lateral Gene Transfer and Its Effects on Microbial Diversity

Yan and Tania recently published a book chapter in the Encyclopedia of Metagenomics entitled "Lateral gene transfer and microbial diversity," with co-author Dr. Rebecca Case, also from the Department of Biological Sciences. The chapter discusses the processes involved in lateral gene transfer, the acquisition of genetic material from individuals that are not an organism's direct cellular parent, and their consequences on the diversity of microbial populations.

Generating genetic diversity in bacteria and archaea (from Nasreen et al., 2013)