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QIIME allows integration and analysis of high-throughput community sequencing data. Nat. Meth.
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The article was published on 2010-01-01 and is currently open access. It has received 963 citations till now. The article focuses on the topics: Throughput (business).read more
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Soil bacterial and fungal communities across a pH gradient in an arable soil.
Johannes Rousk,Erland Bååth,Philip C. Brookes,Christian L. Lauber,Catherine A. Lozupone,J. Gregory Caporaso,Rob Knight,Rob Knight,Noah Fierer,Noah Fierer +9 more
TL;DR: Soils collected across a long-term liming experiment were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria, and both the relative abundance and diversity of bacteria were positively related to pH.
Journal ArticleDOI
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Nicholas A. Bokulich,Benjamin D. Kaehler,Jai Ram Rideout,Matthew R. Dillon,Evan Bolyen,Rob Knight,Gavin A. Huttley,J. Gregory Caporaso +7 more
TL;DR: The results illustrate the importance of parameter tuning for optimizing classifier performance, and the recommendations regarding parameter choices for these classifiers under a range of standard operating conditions are made.
Journal ArticleDOI
Multi-omics approaches to disease.
TL;DR: This review provides an overview of omics technologies and methods for their integration across multiple omics layers and offers the opportunity to understand the flow of information that underlies disease.
Journal ArticleDOI
Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study
Toshitaka Odamaki,Kumiko Kato,Hirosuke Sugahara,Hashikura Nanami,Sachiko Takahashi,Jin-zhong Xiao,Fumiaki Abe,Ro Osawa +7 more
TL;DR: Analysis of gut microbiota composition in newborn to centenarian Japanese subjects revealed certain transition types of microbiota were enriched in infants, adults, elderly individuals and both infant and elderly subjects, and transporter property prediction results suggest that nutrients in the gut might play an important role in changing the Gut microbiota composition with age.
Journal ArticleDOI
Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study
Dae Wook Kang,James B. Adams,Ann C. Gregory,Ann C. Gregory,Thomas J. Borody,Lauren Chittick,Lauren Chittick,Alessio Fasano,Alexander Khoruts,Elizabeth Geis,Juan Maldonado,Sharon McDonough-Means,Elena L. Pollard,Simon Roux,Simon Roux,Michael J. Sadowsky,Karen Schwarzberg Lipson,Matthew B. Sullivan,J. Gregory Caporaso,Rosa Krajmalnik-Brown +19 more
TL;DR: This exploratory, extended-duration treatment protocol appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD.
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more