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Page 1
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: plichta 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.
Identification of specific microbiota members that induce beige fat biogenesis in response to dietary cues.
Honda K, Tanoue T, Nagayama M, Roochana A, Zimmerman S, Ashenberg O, Jain T, Sasajima S, Takeshita K, Hetherington N, Okahashi N, Ueda M, Konishi M, Nakayama Y, Minoda A, Skelly A, Minokoshi Y, Pucci N, Mende D, Arita M, Yamamoto H, Watanabe S, Miura K, Suda W, Atarashi K, Matsushita M, Kajimura S, Plichta D, Saito M, Xavier R. Honda K, et al. Among authors: plichta d. Res Sq [Preprint]. 2024 Dec 3:rs.3.rs-5454144. doi: 10.21203/rs.3.rs-5454144/v1. Res Sq. 2024. Update in: Nature. 2026 Mar 4. doi: 10.1038/s41586-026-10205-3. PMID: 39678347 Free PMC article. Updated. Preprint.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium; Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium. Nielsen HB, et al. Among authors: plichta dr. Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6. Nat Biotechnol. 2014. PMID: 24997787
Commensal consortia decolonize Enterobacteriaceae via ecological control.
Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridoshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda K. Furuichi M, et al. Among authors: plichta dr. Nature. 2024 Sep;633(8031):878-886. doi: 10.1038/s41586-024-07960-6. Epub 2024 Sep 18. Nature. 2024. PMID: 39294375 Free PMC article.
Transcriptional interactions suggest niche segregation among microorganisms in the human gut.
Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O; Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium; Sommer MO, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB. Plichta DR, et al. Nat Microbiol. 2016 Aug 26;1(11):16152. doi: 10.1038/nmicrobiol.2016.152. Nat Microbiol. 2016. PMID: 27564131
Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control.
Honda K, Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta D, Hasegawa N, Ohya T, Bhattarai S, Sasajima S, Yoshimasa A, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Skelly A, Suda W, Hattori M, Nakamoto N, Caballero S, Norman J, Olle B, Tanoue T, Arita M, Bucci V, Atarashi K, Xavier R. Honda K, et al. Among authors: plichta d. Res Sq [Preprint]. 2023 Oct 23:rs.3.rs-3462622. doi: 10.21203/rs.3.rs-3462622/v1. Res Sq. 2023. Update in: Nature. 2024 Sep;633(8031):878-886. doi: 10.1038/s41586-024-07960-6. PMID: 37961431 Free PMC article. Updated. Preprint.
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut.
Roager HM, Hansen LB, Bahl MI, Frandsen HL, Carvalho V, Gøbel RJ, Dalgaard MD, Plichta DR, Sparholt MH, Vestergaard H, Hansen T, Sicheritz-Pontén T, Nielsen HB, Pedersen O, Lauritzen L, Kristensen M, Gupta R, Licht TR. Roager HM, et al. Among authors: plichta dr. Nat Microbiol. 2016 Jun 27;1(9):16093. doi: 10.1038/nmicrobiol.2016.93. Nat Microbiol. 2016. PMID: 27562254
51 results