BISMiS Live 2022

Biosketch: Mark Pallen is Professor of Microbial Genomics at the University of East Anglia and a Research Group Leader at the Quadram Institute in Norwich, UK. For two decades, Pallen has been at the forefront of efforts to apply sequencing and bioinformatics to a range of problems in microbiology, including genomic epidemiology of pathogens and the application of metagenomics in clinical and veterinary microbiology and in ancient DNA research. Recently, Pallen has broken new ground in applying Linnaean binomials to hundreds of new species from animal gut microbiomes and in devising creative new approaches to the generation of new taxonomic names en masse. He has advised the WHO on the use of names for SARS-CoV2 Variants of Concern and helped bacteriophage experts develop hundreds of new names for viral species. Pallen is director of the microbiology cloud-computing CLIMB-BIG- DATA project (https://climb.ac.uk) and of the doctoral training programme, Microbes, Microbiomes and Bioinformatics (https://uea.ac.uk/phd/mmbdtp)

Biosketch: I received my Ph.D from The University of Texas at Austin studying autotrophy in phototrophic bacteria in 1978. Since then, my research has focused on the physiology, systematics and ecology of environmentally important microorganisms. Of special interest is to understand the complete organism, from the biochemical mechanisms it uses to accomplish its day-to-day tasks of living to its interactions with other organisms and its environment. In this context, my work has focused on the methane-producing archaeon Methanococcus, DMSP metabolism in the marine bacterium Ruegeria, and the soil microbiome. I also served as an associate editor of the International Journal of Systematic and Evolutionary Microbiology, 1995-2001; Supervising Editor of Bergey’s Manual of Systematics of Archaea and Bacteria, 2006-2019; Treasurer of International Committee for Systematics of Prokaryotes, 2014-2000; and Treasurer of Bergey’s International Society for Microbial Systematics, 2010-2020.

Biosketch: I am a senior research scientist in National Institute of Advanced Industrial Science and Technology (AIST), Japan. I received my Ph.D degree from the Hokkaido University studying psychrophilic bacteria in permafrost in 2009. I joined at AIST as a postdoc followed by research scientist. One of my research objective is to elucidate the physiology and ecology of microorganisms in deep biosphere, especially those associated with biological methane production, by cultivation methods.

Biosketch: Mauricio Chalita, a computer scientist, attended Seoul National University, where he received his Ph.D. degree in Bioinformatics and developed a high interest in new methods for shotgun metagenomics analysis. In 2017, he started working for Chunlab Inc., the creators of EzBioCloud, where he developed new methods for the analysis of shotgun metagenomic data, focusing on accurate abundance prediction of prokaryotic organisms. In 2021, Chunlab Inc. joined the conglomerate CJ in South Korea, re-naming the company to CJ Bioscience, which focuses on microbial drug discovery. Currently, he is the head of bioinformatics at CJ Bioscience leading the development of a new multi-omics drug discovery platform.

Biosketch: Maria is a molecular microbiologist who turned herself into one of the internationally recognised experts on prokaryotic nomenclature following her interests in formation and application of names. She obtained her doctoral degree in 2011 from the Nuclear Physics Institute in Russia and the University of Grenoble in France. She further acquired most of her professional experience at the University of Queensland in Australia where she still works as a principal taxonomic curator of the Genome Taxonomy Database (or GTDB) for which she overviews all nomenclature related issues and assists in development and validation of curation tools and criteria. Maria is a member of the Judicial Commission of International Committee on Systematics of Prokaryotes and she also played critical role in development of the recently established SeqCode which is aimed to facilitate naming, specifically for uncultured taxa. Together with Prof. Phil Hugenholtz and the rest of GTDB team she continues to pursue the goal of unified taxonomic framework for all prokaryotic taxa.

Biosketch: Patrick Forterre started working on DNA replication and DNA topology in Bacteria. Inspired by Carl Woese’s work, he turned out to study these mechanisms in Archaea (formerly archaebacteria). His first major contribution was the characterization of reverse gyrase, a novel type of DNA topoisomerase that introduces positive superturns into DNA. He could show that reverse gyrase is the only protein essential for life at high temperature. Patrick Forterre defended his Habilitation in 1985 at the University of Paris VII and become Professor at the University of Orsay where he set up his own laboratory in 1989. In 1997, his team discovered the enzyme that triggers meiotic recombination in eukaryotes, SPO11, thanks to their work on archaeal DNA topoisomerase. In 2000, they identified the first DNA replication origin in Archaea. Patrick Forterre was then selected among the few invited speakers at the meeting organized when Carl Woese received the Crafoord prize in 2003 in Stockholm. In 2004, Patrick Forterre became head of the Microbiology Department at the Insitut Pasteur in Paris. He set up in this Institute a new laboratory while still running his laboratory in Orsay. He invited David Prangishvili to work with him on archaeal viruses in Pasteur. They described several new viral families and a fascinating new mechanism of virus egress. Patrick Forterre thought that the importance of viruses was underestimated because they were confused with the virion. He proposed the concept of virocell that posits that viruses transform the infected cell into a new type of cellular organism. In 2014, he received a five years ERC award to study virus-like vesicles in Archaea. The interest of Patrick Forterre for Archaea was early on boosted by their pivotal position in the universal tree of life. He promoted the name LUCA, for the Last Universal Common Ancestor. More recently, he revisited with his coworkers Violette Da Cunha and Morgan Gaia the phylogenies sugggesting that eukaryotes originated from Asgard archaea. Their work supports instead the classical Woese’s tree of life and suggest ancient gene exchanges between Asgard and the ancestors of modern eukaryotes. Patrick Forterre is presently honorary professor at the Institut Pasteur and emeritus Professor at the University Paris-Saclay.

Biosketch: My main research interest is the understanding of eco-evolutionary principles governing microbial communities: evolutionary and ecologic forces shaping populations and their metabolic potential, their interactions with other species, their hosts, and the environment, and the role of stochasticity. In the pursuit of these questions, I’ve garnered ample experience on genomic and metagenomic analyses in environmental, clinical, agricultural, and engineered settings, including the description, characterization, modeling, and simulation of microbial communities and populations. I’ve explored and discussed both theoretical and practical problems on microbiome analysis including the development and application of methods on phylogenomics, taxonomy of prokaryotes, metabolic modeling, statistical techniques, and sequence analyses. I’ve developed tens of bioinformatic tools and web interfaces including grid and cloud computing in a variety of programming languages and frameworks (Ruby, Rails, Perl, R, C++, etc) with over 10,000 downloads or online queries per month, available at https://rodriguez-r.com/software.

Biosketch: My foundational studies and training were under the guidance of Haroun Shah (PhD) and then for 14yrs with David Collins in Reading, UK where as a Senior Research Fellow I was exposed to a plethora of novel organisms and first cut my teeth with the genus Clostridium. My expertise in microbial systematics spans a 37-yr period and I have been responsible or associated with, the naming or reclassification of over 160 bacteria that includes 2 families, 40 genera and almost 100 species. The focus of much of my work is with the gastrointestinal tract of both man and animals. My major academic achievements in bacterial systematics includes a fundamental restructuring of the genus Clostridium and relatives, and the description of many novel taxa from environmental, clinical and veterinary sources. My record of success is demonstrated by my publication record (approx.200) that includes multiple chapters to Bergey’s Manual of Systematics of Archaea and Bacteria, chapters to Biodiversity and Taxonomy of the Lactic Acid Bacteria, The Prokaryotes and the Manual of Clinical Microbiology. From 2010 I was the Associate Editor of the Bulletin of BISMiS and served as Editor in Chief (2012-2019). In 2012, I was appointed to the Editorial Board as an Associate Editor of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) (retired 2019). From 2015 I have taken an active role in the use of in-silico methods to identify and predict chemotaxonomic biomarkers within the genomes of microorganisms. I believe my passion for my subject matter is not only reflected in my research program but also in my active teaching program that extends beyond lectures to the teaching laboratory. In 2018 I was a recipient of a Fulbright Scholar Award in 2021 was awarded the President’s Associates Presidential Professor here at the University of Oklahoma.