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Borenstein DBruce, Ringel P, Basler M, Wingreen NS. Established Microbial Colonies Can Survive Type VI Secretion Assault. PLoS Comput Biol. 2015 ;11(10):e1004520.
Brooks JF, Hooper LV. Interactions among microbes, the immune system, and the circadian clock. Semin Immunopathol. 2020 ;42(6):697-708.
Bushin LB, Covington BC, Rued BE, Federle MJ, Seyedsayamdost MR. 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.
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Chen Y-C, Seyedsayamdost MR, 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.
Claesen J, Spagnolo JB, Ramos SFlores, Kurita KL, Byrd AL, Aksenov AA, et al. A antibiotic modulates human skin microbiota composition in hair follicles. Sci Transl Med. 2020 ;12(570).
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DeCandia AL, Leverett KN, vonHoldt BM. 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.
DeCandia AL, Brenner LJ, King JL, vonHoldt BM. 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.
Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, et al. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020 ;8(1):93.
Donia MS, Fischbach MA. HUMAN MICROBIOTA. Small molecules from the human microbiota. Science. 2015 ;349(6246):1254766.
Donia MS, Cimermancic P, Schulze CJ, Brown LCWieland, Martin J, Mitreva M, et al. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014 ;158(6):1402-1414.
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Erez A, Lopez JG, Weiner BG, Meir Y, Wingreen NS. Nutrient levels and trade-offs control diversity in a serial dilution ecosystem. Elife. 2020 ;9.
Erez A, Lopez JG, Meir Y, Wingreen NS. Enzyme regulation and mutation in a model serial-dilution ecosystem. Phys Rev E. 2021 ;104(4-1):044412.
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Farag MA, Hegazi NM, Donia MS. 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.
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Guo C-J, Chang F-Y, Wyche TP, Backus KM, Acker TM, Funabashi M, et al. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017 ;168(3):517-526.e18.
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Jang C, Hui S, Lu W, Cowan AJ, Morscher RJ, Lee G, et al. The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids. Cell Metab. 2018 ;27(2):351-361.e3.
Javdan B, Lopez JG, Chankhamjon P, Lee Y-CJ, Hull R, Wu Q, et al. Personalized Mapping of Drug Metabolism by the Human Gut Microbiome. Cell. 2020 ;181(7):1661-1679.e22.
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Lopez JG, Wingreen NS. Noisy metabolism can promote microbial cross-feeding. Elife. 2022 ;11.
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Mourani PM, Sontag MK, Williamson KM, J Harris K, Reeder R, Locandro C, et al. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J. 2021 ;57(3).
Mukherjee S, Bassler BL. Bacterial quorum sensing in complex and dynamically changing environments. Nat Rev Microbiol. 2019 ;17(6):371-382.
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Sugimoto Y, Camacho FR, Wang S, Chankhamjon P, Odabas A, Biswas A, et al. A metagenomic strategy for harnessing the chemical repertoire of the human microbiome. Science. 2019 ;366(6471).
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Tuttle RN, Demko AM, Patin NV, Kapono CA, Donia MS, Dorrestein P, et al. Detection of Natural Products and Their Producers in Ocean Sediments. Appl Environ Microbiol. 2019 ;85(8).
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Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, et al. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014 ;16(4):495-503.