Alex Karp

Ann C. Gregory, A. Zayed, N. Conceição-Neto, Ben Temperton, B. Bolduc, A. Alberti, M. Ardyna, K. Arkhipova, Margaux Carmichael, C. Cruaud, C. Dimier, Guillermo Domínguez-Huerta, J. Ferland, S. Kandels, Yunxiao Liu, C. Marec, S. Pesant, M. Picheral, S. Pisarev, J. Poulain, J. Tremblay, D. Vik, M. Babin, C. Bowler, Alexander I. Culley, C. Vargas, B. Dutilh, D. Iudicone, L. Karp‐Boss, S. Roux, S. Sunagawa, P. Wincker, M. Sullivan, S. Acinas, P. Bork, E. Boss, G. Cochrane, M. Follows, G. Gorsky, N. Grimsley, L. Guidi, P. Hingamp, O. Jaillon, S. Kandels-Lewis, E. Karsenti, F. Not, H. Ogata, N. Poulton, J. Raes, C. Sardet, S. Speich, L. Stemmann

Summary: Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

I. Keseler, A. Mackie, Martín Peralta-Gil, Alberto Santos-Zavaleta, S. Gama-Castro, César Bonavides-Martínez, C. Fulcher, Araceli M. Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, I. Schröder, A. Shearer, Pallavi Subhraveti, Michael D. Travers, Deepika Weerasinghe, V. Weiss, J. Collado-Vides, R. Gunsalus, I. Paulsen, P. Karp

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.

A. Shalek, Jacob T. Robinson, Ethan S. Karp, Jin Seok Lee, D. Ahn, Myung‐Han Yoon, Amy A. Sutton, Marsela Jorgolli, Rona S. Gertner, Taranjit S. Gujral, G. MacBeath, E. Yang, Hongkun Park

W. Anderegg, A. Konings, A. Trugman, Kailiang Yu, D. Bowling, Robert Gabbitas, D. Karp, S. Pacala, J. Sperry, B. Sulman, Nicole Zenes

Alborz Mahdavi, L. Ferreira, C. Sundback, J. Nichol, E. Chan, D. Carter, C. Bettinger, Siamrut Patanavanich, Loice Chignozha, E. Ben-Joseph, Alex Galakatos, H. Pryor, I. Pomerantseva, P. Masiakos, W. Faquin, A. Zumbuehl, Seungpyo Hong, J. Borenstein, J. Vacanti, R. Langer, J. Karp