D
Daniel McDonald
Researcher at University of California, San Diego
Publications - 157
Citations - 84726
Daniel McDonald 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 46, co-authored 128 publications receiving 64433 citations. Previous affiliations of Daniel McDonald include University of Colorado Boulder & University of California, Berkeley.
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Journal ArticleDOI
Extreme Dysbiosis of the Microbiome in Critical Illness
Daniel McDonald,Gail Ackermann,Ludmila Khailova,Christine Baird,Daren K. Heyland,Rosemary Kozar,Margot Lemieux,Karrie Derenski,Judy King,Christine Vis-Kampen,Rob Knight,Paul E. Wischmeyer +11 more
TL;DR: The initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, “health-promoting” microbiome and thereby improve patient outcomes.
Journal ArticleDOI
The Microbiome and Human Biology
Rob Knight,Chris Callewaert,Chris Callewaert,Clarisse Marotz,Embriette R. Hyde,Justine W. Debelius,Daniel McDonald,Mitchell L. Sogin +7 more
TL;DR: This review describes how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to new discoveries in microbiome research.
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Balance Trees Reveal Microbial Niche Differentiation
James T. Morton,Jon G. Sanders,Robert A. Quinn,Daniel McDonald,Antonio Gonzalez,Yoshiki Vázquez-Baeza,Jose A. Navas-Molina,Se Jin Song,Jessica L. Metcalf,Embriette R. Hyde,Manuel E. Lladser,Pieter C. Dorrestein,Rob Knight +12 more
TL;DR: It is shown that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum, and have the potential to reshape how future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples are carried out.
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Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins
Elizabeth E. Hansen,Catherine A. Lozupone,Federico E. Rey,Meng Wu,Janaki L. Guruge,Aneesha Narra,Jonathan Goodfellow,Jesse R. Zaneveld,Daniel McDonald,Julia A. Goodrich,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +12 more
TL;DR: It is hypothesized that M. smithii strains use their different repertoires of ALPs to create diversity in their metabolic niches, by allowing them to establish syntrophic relationships with bacterial partners with differing metabolic capabilities and patterns of co-occurrence.
Journal ArticleDOI
PyCogent: a toolkit for making sense from sequence
Rob Knight,Peter Maxwell,Amanda Birmingham,Jason Carnes,J. Gregory Caporaso,Brett C Easton,Michael Eaton,Micah Hamady,Helen Lindsay,Zongzhi Liu,Catherine A. Lozupone,Daniel McDonald,Michael S. Robeson,Raymond Sammut,Sandra Smit,Matthew Wakefield,Matthew Wakefield,Jeremy Widmann,Shandy Wikman,Stephanie A. Wilson,Hua Ying,Gavin A. Huttley +21 more
TL;DR: The COmparative GENomic Toolkit is implemented in Python, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.