D
Dorothy Kim
Researcher at Children's Hospital of Philadelphia
Publications - 6
Citations - 516
Dorothy Kim is an academic researcher from Children's Hospital of Philadelphia. The author has contributed to research in topics: Metabolome & Microbiome. The author has an hindex of 4, co-authored 6 publications receiving 347 citations. Previous affiliations of Dorothy Kim include University of Pennsylvania.
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Journal ArticleDOI
Optimizing methods and dodging pitfalls in microbiome research
Dorothy Kim,Casey E. Hofstaedter,Chunyu Zhao,Lisa M. Mattei,Ceylan Tanes,Erik L. Clarke,Abigail Lauder,Scott Sherrill-Mix,Christel Chehoud,Judith R. Kelsen,Maire A. Conrad,Ronald G. Collman,Robert N. Baldassano,Frederic D. Bushman,Kyle Bittinger +14 more
TL;DR: Suggestions for optimizing experimental design and avoiding known pitfalls are presented, organized in the typical order in which studies are carried out, to help researchers in this exciting field advance their studies efficiently while avoiding errors.
Journal ArticleDOI
Bacterial colonization reprograms the neonatal gut metabolome.
Kyle Bittinger,Chunyu Zhao,Yun Li,Eileen G Ford,Elliot S. Friedman,Josephine Ni,Chiraag Kulkarni,Jingwei Cai,Yuan Tian,Qing Liu,Andrew D. Patterson,Debolina Sarkar,Siu Hung Joshua Chan,Costas D. Maranas,Anumita Saha-Shah,Peder J. Lund,Benjamin A. Garcia,Lisa M. Mattei,Jeffrey S. Gerber,Michal A. Elovitz,Andrea Kelly,Patricia A. DeRusso,Dorothy Kim,Casey E. Hofstaedter,Mark Goulian,Hongzhe Li,Frederic D. Bushman,Babette S. Zemel,Gary D. Wu +28 more
TL;DR: It is shown that the gut is detectably colonized within 16 h of birth, with Escherichia coli dominating, and that this correlates with proteome and metabolome changes including the fermentation of amino acids, which provides a mechanism for the initial growth of E. coli under anaerobic conditions.
Journal ArticleDOI
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease
Frederic D. Bushman,Maire A. Conrad,Yue Ren,Chunyu Zhao,Christopher H Gu,Christopher Petucci,Minsoo Kim,Arwa Abbas,Kevin J. Downes,Nina Devas,Lisa M. Mattei,Jessica Breton,Jessica Breton,Judith R. Kelsen,Judith R. Kelsen,Sarah Marakos,Alissa Galgano,Kelly Kachelries,Jessi Erlichman,Jessica Hart,Michael Moraskie,Dorothy Kim,Huanjia Zhang,Casey E. Hofstaedter,Gary D. Wu,James D. Lewis,Joseph P. Zackular,Joseph P. Zackular,Hongzhe Li,Kyle Bittinger,Robert Baldassano,Robert Baldassano +31 more
TL;DR: In IBD + CDI, both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile are detected, and the most discriminating metabolite found is isocaproyltaurine, which may be useful as a joint marker of the two disease processes.
Journal ArticleDOI
Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals.
Jennifer H. Han,Zena Lapp,Frederic D. Bushman,Frederic D. Bushman,Ebbing Lautenbach,Ellie J. C. Goldstein,Lisa M. Mattei,Casey E. Hofstaedter,Dorothy Kim,Irving Nachamkin,Charles Garrigan,Tanya Jain,Warren B. Bilker,Hannah Wolford,Rachel B. Slayton,Jacqueleen Wise,Pam Tolomeo,Evan S. Snitkin +17 more
TL;DR: The potential for regional infection prevention efforts that are grounded in genomic epidemiology to identify the patients and facilities that make the greatest contribution to regional MDRO prevalence is highlighted, thereby facilitating the design of precision interventions of maximal impact.
Journal ArticleDOI
Effect of topical swallowed steroids on the bacterial and fungal esophageal microbiota in eosinophilic esophagitis
Alain Benitez,Alain Benitez,Ceylan Tanes,Lisa M. Mattei,Casey E. Hofstaedter,Dorothy Kim,Jonathan Gross,Melanie A. Ruffner,Melanie A. Ruffner,Lindsey Albenberg,Lindsey Albenberg,Jonathan M. Spergel,Jonathan M. Spergel,Kyle Bittinger,Kyle Bittinger,Amanda B. Muir,Amanda B. Muir +16 more
TL;DR: Allergen drives class switching to IgE in the nasal mucosa in allergic rhinitis, and Sequential class switching is required for the generation of high affinity IgE antibodies.