R
Rob Knight
Researcher at University of California, San Diego
Publications - 1188
Citations - 322479
Rob Knight is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Microbiome & Biology. The author has an hindex of 201, co-authored 1061 publications receiving 253207 citations. Previous affiliations of Rob Knight include Anschutz Medical Campus & University of Sydney.
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Journal ArticleDOI
Host variables confound gut microbiota studies of human disease.
Ivan Vujkovic-Cvijin,Jack Sklar,Jack Sklar,Lingjing Jiang,Loki Natarajan,Rob Knight,Yasmine Belkaid +6 more
TL;DR: It is demonstrated that for numerous prevalent, high-burden human diseases, matching cases and controls for confounding variables reduces observed differences in the microbiota and the incidence of spurious associations.
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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
Francesco Asnicar,Andrew Maltez Thomas,Francesco Beghini,Claudia Mengoni,Serena Manara,Paolo Manghi,Qiyun Zhu,Mattia Bolzan,Fabio Cumbo,Uyen May,Jon G. Sanders,Jon G. Sanders,Moreno Zolfo,Evguenia Kopylova,Edoardo Pasolli,Edoardo Pasolli,Rob Knight,Siavash Mirarab,Curtis Huttenhower,Nicola Segata +19 more
TL;DR: PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences, and reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers.
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A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system
Jessica L. Metcalf,Laura Wegener Parfrey,Antonio Gonzalez,Christian L. Lauber,Dan Knights,Gail Ackermann,Gregory Humphrey,Matthew J. Gebert,Will Van Treuren,Donna Berg-Lyons,Kyle G. Keepers,Yan Guo,James H. Bullard,Noah Fierer,Noah Fierer,David O. Carter,Rob Knight +16 more
TL;DR: It is shown that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days, and suggested that microbial community data can be developed into a forensic tool for estimating PMI.
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Genetic and environmental control of host-gut microbiota interactions
Elin Org,Brian W. Parks,Jong Wha J. Joo,Benjamin L. Emert,William A. Schwartzman,Eun Yong Kang,Margarete Mehrabian,Calvin Pan,Rob Knight,Robert P. Gunsalus,Thomas A. Drake,Eleazar Eskin,Aldons J. Lusis +12 more
TL;DR: It is concluded that, in a controlled environment, the genetic background accounts for a substantial fraction of abundance of most common microbiota, and loci controlling microbiota composition are mapped and prioritized.
Journal ArticleDOI
Evaluating the Information Content of Shallow Shotgun Metagenomics
Benjamin Hillmann,Gabriel A. Al-Ghalith,Robin R. Shields-Cutler,Qiyun Zhu,Daryl M. Gohl,Kenneth B. Beckman,Rob Knight,Dan Knights +7 more
TL;DR: Shallow shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing, and is recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.