Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

Autor: Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

Publikováno v: mSystems, Vol 7, Iss 2 (2022)

ABSTRACT We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities an

Externí odkaz: https://doaj.org/article/74b34747bb7a480dbd6966ee04b18e87

An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile

Autor: Todd Z. DeSantis, Jean Luc Bodmer, Rachel Steger, Ivette Caro-Aguilar, Justin Kuczynski, Janet Warrington, Jon H. Heinrichs, Todd Schnaufer, Su Wang, Susan Secore, Matthew Miezeiewski, Alexander J. Probst, David S. Thiriot, Irene Rogers, Christel Chehoud, Charlie Hsu, Michele Muravsky

Publikováno v: The ISME Journal. 9:321-332

Clostridium difficile infections (CDI) are caused by colonization and growth of toxigenic strains of C. difficile in individuals whose intestinal microbiota has been perturbed, in most cases following antimicrobial therapy. Determination of the prote

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::61ddb14c62708561aa39c9e07fb18351
https://doi.org/10.1038/ismej.2014.127

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Autor: Jed A. Fuhrman, Justin Kuczynski, Dawn Field, Renzo Kottmann, Jack A. Gilbert, Dan Knights, Lynn M. Schriml, Patrick D. Schloss, Linda A. Amaral-Zettler, Jeroen Raes, Ruth E. Ley, Mark J. Bailey, Jacques Ravel, Andreas Wilke, David A. Relman, Martin J. Blaser, Wolfgang Ludwig, Lindsay K. Newbold, Rob Knight, Josh D. Neufeld, Frederic D. Bushman, Pier Luigi Buttigieg, Peer Bork, Scott T. Kelley, Michelle I. Smith, Norman Morrison, Christopher I. Hunter, Rohini Sinha, Omry Koren, Catherine A. Lozupone, Christian L. Lauber, Diana R. Nemergut, Tanya Yatsunenko, George M. Weinstock, Patrick S. G. Chain, Sara Nakielny, Elizabeth K. Costello, Timothy F. Booth, Anjanette Johnston, Brian D. Muegge, Sarah K. Highlander, Christian Quast, Susanna Assunta-Sansone, Aymé Spor, Bruce W. Birren, Sujeevan Ratnasingham, Peter Sterk, Andrew S. Whiteley, Antonio Gonzalez, Owen White, Robert P. Guralnick, Pelin Yilmaz, Jeffrey I. Gordon, Emily S. Charlson, Doug Wendel, Dirk Gevers, Eamonn Maguire, Erica Sodergren, Ilene Karsch-Mizrachi, Joseph F. Petrosino, Elmar Pruesse, Folker Meyer, Andrew L. Kau, Jörg Peplies, Giriprakash Palanisamy, Richard A. Gibbs, Jerry Kennedy, Doyle V. Ward, Nikos C. Kyrpides, Karen E. Nelson, Wolfgang Hankeln, Manimozhiyan Arumugam, Philippe Rocca-Serra, Philip Hugenholtz, James M. Tiedje, Robert Larsen, Jesse Stombaugh, Rachel E. Gallery, Lita M. Proctor, Janet K. Jansson, Todd Z. DeSantis, Vivien Bonazzi, Anna Oliver, Laura K. Baumgartner, Robert Vaughan, James R. Cole, Joonhong Park, Frank Oliver Glöckner, Donna Lyons, Heather Huot-Creasy, Teresa M. Legg, Norman R. Pace, Noah Fierer, Jennifer R. Wortman, Barbara A. Methé, Inigo San Gil, Guy Cochrane, Peter Dawyndt

Publikováno v: Nature Biotechnology. 29:415-420

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e4ce19a957f3247a7a2d5328a104024
https://doi.org/10.1038/nbt.1823

Bayesian community-wide culture-independent microbial source tracking

Autor: Michael C. Mozer, Jesse R. Zaneveld, Frederic D. Bushman, Rob Knight, Emily S. Charlson, Scott T. Kelley, Dan Knights, Justin Kuczynski, Ronald G. Collman

Publikováno v: Nature Methods. 8:761-763

Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community tha

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::189a1336193000208822e65dd0ab7d4c
https://doi.org/10.1038/nmeth.1650

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Autor: Susan M. Huse, Rob Knight, Jose C. Clemente, Jesse Stombaugh, Justin Kuczynski, John Hufnagle, Folker Meyer, J. Gregory Caporaso, Daniel McDonald, Doug Wendel, Jai Ram Rideout, Andreas Wilke

Publikováno v: GigaScience
GigaScience, vol 1, iss 1
McDonald, D; Clemente, JC; Kuczynski, J; Rideout, JR; Stombaugh, J; Wendel, D; et al.(2012). The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. GigaScience, 464(1). doi: 10.1186/2047-217X-1-7. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/565380jb
GigaScience, Vol 1, Iss 1, p 7 (2012)

Background: We present the Biological Observation Matrix (BIOM, pronounced " biome" ) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8aa7ac9fb0263ae361f78934fc2ac1c9
https://doi.org/10.1186/2047-217x-1-7