Blaser Martin J.

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Blaser
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Martin J.
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  • Preprint
    Current understanding of the human microbiome
    ( 2018-02-05) Gilbert, Jack A. ; Blaser, Martin J. ; Caporaso, J. Gregory ; Jansson, Janet K. ; Lynch, Susan V. ; Knight, Rob
    Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.
  • Article
    Toward a predictive understanding of Earth’s microbiomes to address 21st century challenges
    (American Society for Microbiology, 2016-05-13) Blaser, Martin J. ; Cardon, Zoe G. ; Cho, Mildred K. ; Dangl, Jeffery ; Donohue, Timothy J. ; Green, Jessica L. ; Knight, Rob ; Maxon, Mary E. ; Northen, Trent R. ; Pollard, Katherine ; Brodie, Eoin L.
    Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.
  • Preprint
    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
    ( 2011-01-04) Yilmaz, Pelin ; Kottmann, Renzo ; Field, Dawn ; Knight, Rob ; Cole, James R. ; Amaral-Zettler, Linda A. ; Gilbert, Jack A. ; Karsch-Mizrachi, Ilene ; Johnston, Anjanette ; Cochrane, Guy R. ; Vaughan, Robert ; Hunter, Christopher ; Park, Joonhong ; Morrison, Norman ; Rocca-Serra, Philippe ; Sterk, Peter ; Arumugam, Manimozhiyan ; Bailey, Mark ; Baumgartner, Laura ; Birren, Bruce W. ; Blaser, Martin J. ; Bonazzi, Vivien ; Booth, Tim ; Bork, Peer ; Bushman, Frederic D. ; Buttigieg, Pier Luigi ; Chain, Patrick S. G. ; Charlson, Emily ; Costello, Elizabeth K. ; Huot-Creasy, Heather ; Dawyndt, Peter ; DeSantis, Todd ; Fierer, Noah ; Fuhrman, Jed A. ; Gallery, Rachel E. ; Gevers, Dirk ; Gibbs, Richard A. ; San Gil, Inigo ; Gonzalez, Antonio ; Gordon, Jeffrey I. ; Guralnick, Robert P. ; Hankeln, Wolfgang ; Highlander, Sarah ; Hugenholtz, Philip ; Jansson, Janet K. ; Kau, Andrew L. ; Kelley, Scott T. ; Kennedy, Jerry ; Knights, Dan ; Koren, Omry ; Kuczynski, Justin ; Kyrpides, Nikos C. ; Larsen, Robert ; Lauber, Christian L. ; Legg, Teresa ; Ley, Ruth E. ; Lozupone, Catherine A. ; Ludwig, Wolfgang ; Lyons, Donna ; Maguire, Eamonn ; Methe, Barbara A. ; Meyer, Folker ; Muegge, Brian ; Nakielny, Sara ; Nelson, Karen E. ; Nemergut, Diana ; Neufeld, Josh D. ; Newbold, Lindsay K. ; Oliver, Anna E. ; Pace, Norman R. ; Palanisamy, Giriprakash ; Peplies, Jorg ; Petrosino, Joseph ; Proctor, Lita ; Pruesse, Elmar ; Quast, Christian ; Raes, Jeroen ; Ratnasingham, Sujeevan ; Ravel, Jacques ; Relman, David A. ; Assunta-Sansone, Susanna ; Schloss, Patrick D. ; Schriml, Lynn M. ; Sinha, Rohini ; Smith, Michelle I. ; Sodergren, Erica ; Spor, Ayme ; Stombaugh, Jesse ; Tiedje, James M. ; Ward, Doyle V. ; Weinstock, George M. ; Wendel, Doug ; White, Owen ; Whiteley, Andrew ; Wilke, Andreas ; Wortman, Jennifer R. ; Yatsunenko, Tanya ; Glockner, Frank Oliver
    Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The “environmental packages” apply to any sequence whose origin is known and can therefore be used in combination with MIMARKS or other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we establish the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.