CRISPR ecology and evolution

Francisco JM Mojica (born 5 October 1963, Elche, Spain) earned his PhD in Biology from the University of Alicante (Spain) in 1993. Afterwards, he carried out postdoctoral research work at the University of Utah (USA; 1993) and the University of Oxford (UK; 1995-1996). In 1997, he returned to the University of Alicante to hold a faculty position as professor of Microbiology. His pioneering work on CRISPR since the early 1990s has been recognized with many prestigious awards, including the Rey Jaime I Basic Research Prize, the Lilly Foundation Award for Preclinical Biomedical Research, the BBVA Foundation Frontiers of Knowledge Award in Biomedicine, the PLuS Alliance Prize for Global Innovation, and the Albany Medical Center Prize in Biomedical Research.

Eugene V Koonin is leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information (NIH) and member of the National Academy of Sciences of the USA. The American Academy of Arts and Sciences, American Academy of Microbiology and The European Molecular Biology Organization. He received his PhD in Molecular Biology in 1983 from Moscow State University, joined the NCBI in 1991 and became a Senior Investigator in 1996. His research interests focus on evolutionary genomics of prokaryotes, eukaryotes and viruses, host-parasite coevolution and general theory of the evolution of life.

Eduardo Rocha did MScs in Chemical Engineering and Applied Maths, a PhD in Bioinformatics and an Habilitation in Biology. He is a senior researcher at CNRS and head of the Microbial Evolutionary Genomics unit at Pasteur Institute. He is a Specialist in comparative genomics, in particular in the use of bioinformatics and biostatistics techniques to study microbial evolution. His research aims at understanding how and why genomes are organized, and how such organizational features evolve in respect to genome dynamics. In the last decade, his work has focused on the role of mobile genetic elements in driving their host evolution through horizontal gene transfer and how that affects the genomes of both Bacteria and their mobile elements.

Kimberley Seed is an Assistant Professor in the Plant and Microbial Biology Department at the University of California, Berkeley. She earned her Bachelor of Science degree in 2004 from the University of Alberta, her Doctor of Philosophy in Microbiology and Biotechnology under Dr Jonathan Dennis in 2009 from the University of Alberta, and did postdoctoral training in Dr Andrew Camilli’s laboratory at Tufts University School of Medicine in the Department of Molecular Biology & Microbiology. She was a faculty member at the University of Michigan in the Department of Molecular, Cellular and Developmental Biology from 2014-2016 before moving to UC Berkeley. Professor Seed’s laboratory investigates how bacterial pathogens and predatory phages co-evolve. The current major focus of the lab is towards an understanding of how phages impact the evolution and selection of epidemic Vibrio cholerae, the causative agent of cholera.

Peter Fineran is an Associate Professor in the Department of Microbiology and Immunology at the University of Otago, New Zealand. Peter has established an international reputation for his research on the interactions between bacteriophages and other mobile elements and their bacterial hosts. A major focus of his lab are the CRISPR-Cas adaptive prokaryotic immune systems. He obtained a BSc (Hons) in Biochemistry from the University of Canterbury, NZ. He completed his PhD at the University of Cambridge, UK followed by a Post-Doc fellowship. He has made critical contributions to understanding CRISPR-Cas systems, such as how these systems acquire new immune memories and uncovering the mechanisms of CRISPR-Cas regulation. Peter has received many awards in recognition of his research contributions, such as a Rutherford Discovery Fellowship from the Royal Society of New Zealand and the Ross Crozier Medal from the Genetics Society of AustralAsia.

Stan JJ Brouns (1978) is a Molecular Microbiologist who studied Molecular Life Sciences and obtained his PhD from Wageningen University in the Netherlands in 2007. From 2006 he has been interested bacteriophage resistance elucidating the mechanism of CRISPR-mediated bacteriophage defense in prokaryotes. In 2011 he started his own group at the Laboratory of Microbiology (Wageningen University) studying microbe-bacteriophage relationships after obtaining national (VIDI) and European funding (ERC). Dr. Brouns obtained a tenured Associate Professor position at the Kavli Institute of Nanoscience of Delft University of Technology and is still affiliated with Wageningen University. He has contributed to over 60 scientific publications, and has received a number of awards for his pioneering CRISPR work. His lab is interested in the interaction between microbes and viruses and studies the mechanisms that bacteria and archaea use to protect themselves from virus infection including CRISPR. His lab explores the adaptations that viruses have evolved to avoid defense systems and engineers bacteriophages for phage therapy applications.

My laboratory is broadly interested in how viral symbiosis and virus-host co-evolution shape evolutionary processes in natural populations. We combine natural history and population genomics with experimental biology by bringing wild viruses and hosts into lab the for experimental evolution and genetics. We utilize the CRISPR-Cas adaptive immune system a molecular marker to track evolution of viruses and hosts and as a mediator of their interactions. We work in comparative systems of island populations including the archaeaon Sulfolobus islandicus and chronic bacterial infections in CF patients by Pseudomonas aeruginosa. Using modeling predictions and comparative analyses of parameters in each system we test the generality of our models for evolutionary ecology of viruses of microbes. I have extended our conceptual frame-work to include dynamics of microbes and their genetic elements in a one-health context by establishing the new integrated theme called Infection Genomics for One Health (IGOH) at the Carl R. Woese Institute of Genomic Biology. The goal of our theme is to integrate lessons learned from a diversity of systems to develop models of genomic epidemiology to address critical global challenges such as the evolution of antimicrobial resistance and the emergence of infectious disease.

I was promoted to Professor of Microbiology in 2018 and am the Theme Leader of the Infection Genomics for One Health Theme at the Carl R. Woese Institute for Genomic Biology. In 2016 I received an Allen Distinguished Investigator award to model virus-host interactions in microbial populations. In addition, my work has been funded by the NSF, NASA, the Gates Foundation and the Cystic Fibrosis Foundation. I just completed my first year as the Director of the Microbial Diversity Course at the MBL in Woods Hole, MA.

Sylvain Moineau is a Professor in the Department of Biochemistry, Microbiology and Bioinformatics at the Université Laval. He also holds the Canada Research Chair in Bacteriophages and is the Curator of the Félix d’Hérelle Reference Center for Bacterial Viruses, the world largest collection of reference phages. His research group studies phage biology and phage-bacteria interactions. Among others, he has characterized mechanisms used by bacteria to resist phages, including his landmark work on CRISPR-Cas systems. Professor Moineau has won several teaching and research awards. In 2017, he was awarded the NSERC John C. Polanyi Award, the Canadian Society of Microbiologists Murray Award for Career Achievement and the DuPont Excellence Medal. He was elected to the Academy of Sciences of the Royal Society of Canada and appointed an Officer of the Order of Canada. Thomson Reuters and Clarivate Analytics have ranked him amongst the most cited microbiologists for the past four years.

Joe attended the University of Waterloo for his undergrad in Biology and Microbiology, and spent time as a co-op student in labs at Western University (London, ON) and McGill University (Montreal, QC). Joe then attended the University of Toronto to complete his PhD in Alan Davidson's lab where he studied interactions between bacteriophages and their host bacteria, focusing on the effects of lysogeny and the CRISPR-Cas immune system. In the spring of 2015, Joe started his lab at UCSF as a Faculty Fellow. In 2017, Joe continued at UCSF as an Assistant Professor in the Department of Microbiology & Immunology. The lab is currently focused on studying the roles of CRISPR-Cas immune systems in their host organisms, discovering novel CRISPR-Cas functions and identifying ways in which these systems interact with bacteriophages.

Dr Sundberg is a senior lecturer and a PI at the Department of Biological and Environmental Science and Nanoscience Center in University of Jyväskylä, Finland. During 2013-2018 she held the Academy Researcher position in the Centre of Excellence in Biological Interactions, and focused on multirophic coevolutionary dynamics of metazoan-bacterium and bacterium-phage interactions. More recently, Sundberg has studied phage evolution and bacterial CRISPR immunity in freshwater systems and in settings relevant to intensive aquaculture. For example, her studies on the phage-bacterium coevolution in the fish pathogen Flavobacterium columnare have shown that the coevolutionary arms race in the environment selects for increased host range and infectivity in the phage. Molecular understanding of these interactions in aquaculture brings insight also on the development of phage therapy.

I am an evolutionary biologist with a broad general interest ranging from theoretical population genetics, and mathematical epidemiology, to behavioral and evolutionary ecology. I use both theoretical and experimental approaches to study the ecology and evolution of host-parasite interactions. I studied the influence of spatial structure and migration on host-parasite coevolution and local adaptation. I am also interested in the impact of therapeutic interventions like drugs or vaccines on the evolution of pathogens. I am currently working on two experimental models: (1) the coevolution between bacteria and their bacteriophages and (2) the evolutionary ecology of avian malaria.

After his PhD in the lab of Prof. John van der Oost at Wageningen University on the molecular mechanism and regulation of CRISPR-Cas immune systems (2009-2013), Dr. Westra started to explore the evolutionary ecology of CRISPR-Cas immune systems as a Marie-Curie Fellow in the lab of Prof. Angus Buckling, University of Exeter (2013-2015). He then received a NERC Independent Research Fellowship in 2015 to set up his own lab at the University of Exeter, and received further funding from NERC, BBSRC, Wellcome Trust, Leverhulme Trust and ERC.

Austin Burt is Professor of Evolutionary Genetics at Imperial College London. In 2003 he proposed that enzymes that recognise and cut specific sequences of DNA could be used to control pest populations, and since 2005 he has been Principle Investigator of a research consortium developing this idea to control the mosquitoes that transmit malaria, with particular attention to sub-Saharan Africa. Target Malaria is a not-for-profit consortium that currently includes over 100 individuals at 14 institutions across 3 continents (www.targetmalaria.org).