Lu J, Hamblen E, Brenner L, King J, vonHoldt B, DeCandia A. Ear mite infection restructures otic microbial networks in conservation-reliant Santa Catalina Island foxes (Urocyon littoralis catalinae). Mol Ecol. 2023;32(4):892–903. PMID: 36435981

Lopez J, Wingreen N. Noisy metabolism can promote microbial cross-feeding. Elife. 2022;11. PMCID: PMC8983042

Erez A, Lopez J, Meir Y, Wingreen N. Enzyme regulation and mutation in a model serial-dilution ecosystem. Phys Rev E. 2021;104(4-1):044412. PMID: 34781576

Brooks J, Hooper L. Interactions among microbes, the immune system, and the circadian clock. Semin Immunopathol. 2020;42(6):697–708. PMID: 33033938

Bushin L, Covington B, Rued B, Federle M, Seyedsayamdost M. Discovery and Biosynthesis of Streptosactin, a Sactipeptide with an Alternative Topology Encoded by Commensal Bacteria in the Human Microbiome. J Am Chem Soc. 2020;142(38):16265–16275. PMID: 32845143

Chen Y-C, Seyedsayamdost M, Ringstad N. A microbial metabolite synergizes with endogenous serotonin to trigger reproductive behavior. Proc Natl Acad Sci U S A. 2020;117(48):30589–30598. PMCID: PMC7720207

Claesen J, Spagnolo J, Ramos S, Kurita K, Byrd A, Aksenov A, Melnik A, Wong W, Wang S, Hernandez R, Donia M, Dorrestein P, Kong H, Segre J, Linington R, Fischbach M, Lemon K. A antibiotic modulates human skin microbiota composition in hair follicles. Sci Transl Med. 2020;12(570). PMCID: PMC8478231

Mourani P, Sontag M, Williamson K, Harris K, Reeder R, Locandro C, Carpenter T, Maddux A, Ziegler K, Simões E, Osborne C, Ambroggio L, Leroue M, Robertson C, Langelier C, DeRisi J, Kamm J, Hall M, Zuppa A, Carcillo J, Meert K, Sapru A, Pollack M, McQuillen P, Notterman D, Dean M, Wagner B, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network (CPCCRN), Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network (CPCCRN) members are as follows:. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J. 2021;57(3). PMCID: PMC7979474

Erez A, Lopez J, Weiner B, Meir Y, Wingreen N. Nutrient levels and trade-offs control diversity in a serial dilution ecosystem. Elife. 2020;9. PMCID: PMC7486120

Farag M, Hegazi N, Donia M. Molecular networking based LC/MS reveals novel biotransformation products of green coffee by ex vivo cultures of the human gut microbiome. Metabolomics. 2020;16(8):86. PMID: 32748036

Doane M, Morris M, Papudeshi B, Allen L, Pande D, Haggerty J, Johri S, Turnlund A, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery A, Lima L, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards R, Dinsdale E. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020;8(1):93. PMCID: PMC7293782

Javdan B, Lopez J, Chankhamjon P, Lee Y-C, Hull R, Wu Q, Wang X, Chatterjee S, Donia M. Personalized Mapping of Drug Metabolism by the Human Gut Microbiome. Cell. 2020;181(7):1661–1679.e22. PMCID: PMC8591631

DeCandia A, Brenner L, King J, vonHoldt B. Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae). Mol Ecol. 2020;29(8):1463–1475. PMID: 31821650

Sugimoto Y, Camacho F, Wang S, Chankhamjon P, Odabas A, Biswas A, Jeffrey P, Donia M. A metagenomic strategy for harnessing the chemical repertoire of the human microbiome. Science. 2019;366(6471). PMID: 31582523

DeCandia A, Leverett K, vonHoldt B. Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites. Parasit Vectors. 2019;12(1):488. PMCID: PMC6796464

Tuttle R, Demko A, Patin N, Kapono C, Donia M, Dorrestein P, Jensen P. Detection of Natural Products and Their Producers in Ocean Sediments. Appl Environ Microbiol. 2019;85(8). PMCID: PMC6450032

Mukherjee S, Bassler B. Bacterial quorum sensing in complex and dynamically changing environments. Nat Rev Microbiol. 2019;17(6):371–382. PMCID: PMC6615036

Jang C, Hui S, Lu W, Cowan A, Morscher R, Lee G, Liu W, Tesz G, Birnbaum M, Rabinowitz J. The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids. Cell Metab. 2018;27(2):351–361.e3. PMCID: PMC6032988

Guo C-J, Chang F-Y, Wyche T, Backus K, Acker T, Funabashi M, Taketani M, Donia M, Nayfach S, Pollard K, Craik C, Cravatt B, Clardy J, Voigt C, Fischbach M. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017;168(3):517–526.e18. PMCID: PMC5302092

Williams B, Van Benschoten A, Cimermancic P, Donia M, Zimmermann M, Taketani M, Ishihara A, Kashyap P, Fraser J, Fischbach M. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014;16(4):495–503. PMCID: PMC4260654

Donia M, Cimermancic P, Schulze C, Brown L, Martin J, Mitreva M, Clardy J, Linington R, Fischbach M. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014;158(6):1402–1414. PMCID: PMC4164201

Donia M, Fischbach M. HUMAN MICROBIOTA. Small molecules from the human microbiota. Science. 2015;349(6246):1254766. PMCID: PMC4641445

Borenstein D, Ringel P, Basler M, Wingreen N. Established Microbial Colonies Can Survive Type VI Secretion Assault. PLoS Comput Biol. 2015;11(10):e1004520. PMCID: PMC4619000