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Industrialization drives convergent microbial and physiological shifts in the human metaorganism.
Poyet M, Rühlemann M, Schaan AP, Ma Y, Moitinho-Silva L, Wacker EM, Jebens H, Patel L, Nguyen LTT, Zimmer A, Plichta D, McDonald D, Stevens C, Agyei A, Afihene MY, Asibey SO, Awuku YA, Badiane AS, Ching LS, Corzett C, Deme A, Dominguez-Rodrigo M, Duah A, Fezeu A, Froment A, Gibbons S, Girard C, Hooker J, Ibrahim F, Iqaluk D, Juimo V, Kettunen P, Lafosse S, Lango-Yaya E, Lehtimäki J, Lim YAL, Mabulla A, Mahachai V, Mohamed RS, Moniz K, Mwikarago IE, Nartey YA, Ndiaye D, Noel M, Onyekwere C, Pin TM, Plymoth A, Roberts L, Ruokolainen L, Rusine J, Segurel L, Shapiro BJ, Sigwazi S, Sistiaga A, Valles K, Vatanen T, Vilaichone RK, Rosenstiel P, Baines J, Franke A, Ellinghaus D, Knight R, Daly M, Xavier RJ, Alm EJ, Groussin M. Poyet M, et al. Among authors: mcdonald d. bioRxiv [Preprint]. 2025 Oct 20:2025.10.20.683358. doi: 10.1101/2025.10.20.683358. bioRxiv. 2025. PMID: 41280098 Free PMC article. Preprint.
Environmental and maternal imprints on infant gut metabolic development.
Kvitne KE, Allaband C, Onuora JC, Perry D, Zuffa S, Patel L, Charron-Lamoureux V, Mohanty I, Sejane K, Patan A, Mahmud AA, Ahmed T, Bassani DG, González A, Hamer DH, Haque R, Ho B, Hossain MI, Islam MS, McDonald D, Pell LG, Qamar H, Roth DE, Saha S, Shah PS, Siddiqui MM, Sarker SA, Sultana S, Thomas S, Burnett LA, Tsunoda SM, Bode L, Dorrestein PC, Knight R. Kvitne KE, et al. Among authors: mcdonald d. Cell Host Microbe. 2025 Dec 10;33(12):2130-2147.e7. doi: 10.1016/j.chom.2025.11.002. Epub 2025 Nov 26. Cell Host Microbe. 2025. PMID: 41308639 Free PMC article.
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R. Guccione C, et al. Among authors: mcdonald d. Nat Commun. 2025 Jan 18;16(1):825. doi: 10.1038/s41467-025-56077-5. Nat Commun. 2025. PMID: 39827261 Free PMC article.
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns.
Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R. Salido RA, et al. Among authors: mcdonald d. Cell. 2025 Apr 3;188(7):2022-2041.e23. doi: 10.1016/j.cell.2025.01.039. Epub 2025 Feb 27. Cell. 2025. PMID: 40020666 Free article.
Calculating fast differential genome coverages among metagenomic sources using micov.
Weng Y, Guccione C, McDonald D, Oles R, Devkota S, Kopylova E, Sepich-Poore GD, Salido RA, Din MO, Song SJ, Curtius K, Chu H, Bartko A, Hasty J, Knight R. Weng Y, et al. Among authors: mcdonald d. Commun Biol. 2025 Nov 20;8(1):1624. doi: 10.1038/s42003-025-09007-6. Commun Biol. 2025. PMID: 41266796 Free PMC article.
1,815 results