100K Pathogen Genome Project

Genomes and metagenomes are released to the SRA and GenBank via the 100K BioProject (PRJNA186441). Genomes and metagenomes are announced in manuscripts and genome releases.

• Weimer, Bart C. 2017. 100K Pathogen Genome Project. Genome Announcements 5:e00594-17 (invited commentary) (PMID: 28705971) – this describes the project and how it runs.

Genome Releases:

Salmonella – 

• Heithoff, Douglas M. William R. Shimp, John K. House, Yi Xie, Bart C. Weimer, Robert L. Sinsheimer, and Michael J. Mahan. 2012. Intraspecies variation in the emergence of hyper-infectious bacterial strains in nature. PLoS Pathogen 8(4):e1002647 (PMID: 22511871).
• Kong, Nguyet, Narine Arabyan, Kao Thao, Whitney Ng, Bihua C. Huang, Dylan Bobby Storey, Poyin Chen, Allison M. Weis, Soraya Foutouhi, Azarene Foutouhi, Yi Xie, and Bart C. Weimer. 2017. Draft genome sequences of 1183 Salmonella from the 100K Pathogen Genome Project. Genome Announcements 5:e00518-17. (PMID: 28705963).
• Rheault, Jean-Guillaume Emond, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Anna Colavecchio, Virginie Barrere, Brigitte Cadieux, Maud Kerhoas, Alanna Crouse, Lei Zhu, Line Larivière, Ana Victoria Pilar, Camille Cavestri, Travis K. Chapin, Denise Tremblay, Caroline Vincent, Eric Fournier, Khadija Youfsi, Ida Ngueng-Feze, Lingqiao Song, Valentine Usongo, Florence Doualla-Bell, Chrystal Berry, Aleisha R. Reimer, Nguyet Kong, Carol B. Huang, Karen Fong, Emily D. Wilson, Kakali Mukhopadhyay, Walid Mottawea, Dele Ogunremi, Hongsheng Huang, Gitanjali Arya, Ann Perets, Catherine Yoshida, James Robertson, Joel Weadge, Michelle D. Danyluk, John Rohde, Rafael Garduno, Siyun Wang, Céline Nadon, Paul Thomassin,Yann Joly, Ismail Fliss, Gisèle Lapointe, Linda Harris, Roger Stephan, Elton Burnett, Sylvain Moineau, Sandeep Tamber, Sadjia Bekal, France Daigle, Samantha Gruenheid, Danielle Malo, Thomas Wittum, Pascal Delaquis, Alexander Gill, Kenneth E. Sanderson, Martin Wiedmann, Eelco Franz, Lucas Wijnands, Bart C. Weimer, Lawrence Goodridge, and Roger C. Levesque. 2017. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Frontiers in Microbiology 8:996. (PMID: 28626454) Special issue on food safety
• Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft genomes of Salmonella enterica sv Typhimurium LT2 with deleted chitinases that are emerging virulence factors. Genome Announcements 5:e00659-17 (PMID:28774970).
• Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft Genomes of Salmonella lysozyme knockouts. Genome Announcements 5:e00519-17. (PMID: 28596411).
• Arabyan, Narine, Allison M. Weis, Bihua C. Huang and Bart C. Weimer. 2017. Implications of sialidases in diseases: Genome release of Salmonella sialidase knockout strains. Genome Announcements 5:e00341-17. (PMID: 28495784)

Listeria – 

• Chen, Poyin, Henk C. den Bakker, Jonas Korlach, Meredith Ashby, Tyson Clark, Khai Luong, R. J. Roberts, Martin Wiedmann, and Bart C. Weimer. 2017. Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes. App. Environ. Microbiol. 83:e02091-16. (PMID: 27836852).
• Chen, Poyin, Nguyet Kong, Bihua Huang, Kao Thao, Whitney Ng, Dylan Bobby Storey, Narine Arabyan, Azarene Foutouhi, Soraya Foutouhi, and Bart C. Weimer. 100K Pathogen Genome Project: 306 Listeria draft genomes for food safety and public health. 2017. Genome Announcements 5:e00967-16. (PMID: 28183778).

Campylobacter – 

• Weis, Allison M., Kristen A. Clothier, Bihua C. Huang, Nguyet Kong, and Bart C. Weimer. 2017. Multidrug-resistant abortive Campylobacter jejuni draft genome from Northern California. Genome Announcements 5:e00171-17. (PMID: 28408683)
• Weis, Allison M., Bihua C. Huang, Dylan B. Storey, Nguyet Kong, Poyin Chen, Narine Arabyan, Brent Gilpin, Carl Mason, Andrea K. Townsend, Woutrina A. Miller, Barbara A. Byrne, Conor C. Taff, and Bart C. Weimer. 2017. Large-scale release of Campylobacter draft genomes; resources for food safety and public health from the 100K Pathogen Genome Project. Genome Announcements 5(1):e00925-16. (PMID: 28057746).
• Weis, Allison M., Dylan B. Storey, Conor C. Taff, Andrea K. Townsend, Bihua C. Huang, Nguyet T. Kong, Kristin A. Clothier, Abigail Spinner, Barbara A. Byrne, Bart C. Weimer.2016. Genomic comparison of Campylobacter and their potential for zoonotic transmission between birds, primates, and livestock. App. Environ. Microbiol. 82:7165-7175.(PMID: 27736787)
• Taff, Conor C., Allison M. Weis, Chris Barker, Walter M. Boyce, Mitchell G. Hinton, Melissa Jones, Ryane Logsdon, Woutrina A. Smith, Bart C. Weimer, Sarah Wheeler, and Andrea K. Townsend 2016. Influence of host ecology and behavior on Campylobacter jejuni prevalence and environmental contamination risk in a synanthropic wild bird. App. Environ. Microbiol. 82:4811-4820. (PMID: 27260356)

Helicobacter – 

• Draper, Jenny L., Lori M. Hansen, David Bernick, Samar Abedrabbo, Jason G. Underword, Nguyet Kong, Carol B. Huang, Allison M. Weis, Bart C. Weimer, Arnoud Van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemann. 2017. Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains. mBio 8:e02321-16. (PMID: 28223462).

Vibrio – 

• Lüdeke, Catharina H.M., Nguyet Kong, Bart C. Weimer, Markus Fischer, Jessica L. Jones. 2015. Complete genome sequences of a clinical and an environmental Vibrio parahaemolyticus isolate. Genome Announcements. 3(2):e00216-15. (PMID: 25814612)

Shigella –

• Weis, Allison M., Brent Gilpin, Bihua C. Huang, Nguyet Kong, Poyin Chen, and Bart C. Weimer. 2017. Shigella draft genomes: resources for food safety and public health. Genome Announcements 5:e00176-17. (PMID: 28428292)

Informatic approaches:

• Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M Weis, Bihua C. Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2017. Microbiogeography and microbial genome evolution. arXiv:1703.07454 [q-bio.GN]. *co-corresponding author
• Edlund, Stefan, Kristen L. Beck, Niina Haiminen, Laxmi Parida, Dylan Bobby Storey, Bart C. Weimer, James H. Kaufman, David Chambliss. 2016. Design of the MCAW Compute Service for Food Safety Bioinformatics. IBM Journal of Research and Development, 60 (5/6):2.1-2.12 (DOI: 10.1147/JRD.2016.2584798).
• Weimer, Bart C., Dylan Bobby Storey, Christopher A. Elkins, Robert C. Baker, Peter Markwell, David Chambliss, Stefan Edlund, James H. Kaufman. 2016. Defining the food microbiome for authentication, safety, and process management.  IBM Journal of Research and Development, 60 (5/6):1.1-1.13. (DOI: 10.1147/JRD.2016.2582598).
• Dhanasekaran, A. Ranjitha, Jon L. Pearson, Balasubramanian Ganesan, and Bart C. Weimer. 2015. Metabolome Searcher: A high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and metabolites. BMC Bioinformatics 16:62 (DOI: 10.1186/s12859-015-0462-y). (PMID: 25887958)

Metagenome releases:

on the way…