Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.

Nishijima S, Stankevic E, Aasmets O, Schmidt TSB, Nagata N, Keller MI, Ferretti P, Juel HB, Fullam A, Robbani SM, Schudoma C, Hansen JK, Holm LA, Israelsen M, Schierwagen R, Torp N, Telzerow A, Hercog R, Kandels S, Hazenbrink DHM, Arumugam M, Bendtsen F, Brøns C, Fonvig CE, Holm JC, Nielsen T, Pedersen JS, Thiele MS, Trebicka J, Org E, Krag A, Hansen T, Kuhn M, Bork P, GALAXY and MicrobLiver Consortia

Cell, 2025

doi:10.1016/j.cell.2024.10.022.

A catalog of small proteins from the global microbiome.

Duan Y, Santos-Júnior CD, Schmidt TS, Fullam A, de Almeida BLS, Zhu C, Kuhn M, Zhao XM, Bork P, Coelho LP

Nature communications, 2024

doi:10.1038/s41467-024-51894-6.

Discovery of antimicrobial peptides in the global microbiome with machine learning.

Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP

Cell, 2024

doi:10.1016/j.cell.2024.05.013.

Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.

Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J, MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium

Alimentary Pharmacology and Therapeutics, 2024

doi:10.1111/apt.17899.

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P

Nucleic acids research, 2023

doi:10.1093/nar/gkad943.

Computational exploration of the global microbiome for antibiotic discovery.

Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez del Río Á, Schmidt TS, Chong H, Fullam A, Michael K, Zhu C, Houseman A, Somborski J, Vines A, Zhao X, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP

bioRxiv, 2023

doi:10.1101/2023.08.31.555663.

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.

Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR

Nucleic acids research, 2023

doi:10.1093/nar/gkac1078.

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants.

Ferretti P, Wirbel J,Maistrenko OM, Van Rossum T, Alves R, Fullam A, Akanni W, Schudoma C, Schwarz A, Thielemann R, Thomas L, Kandels S, Hercog R, Telzerow A, Letunic I, Kuhn M, Zeller G, Schmidt SBT, Bork P

bioRxiv, 2022

doi:10.1101/2022.02.16.480740.

Drivers and determinants of strain dynamics following fecal microbiota transplantation.

Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P

Nature medicine, 2022

doi:10.1038/s41591-022-01913-0.

A faecal microbiota signature with high specificity for pancreatic cancer.

Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, MAGIC Study investigators, PanGenEU Study investigators, Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P

Gut, 2022

doi:10.1136/gutjnl-2021-324755.

A previously undescribed highly prevalent phage identified in a Danish enteric virome catalog.

Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J

mSystems, 2021

doi:10.1128/mSystems.00382-21.

GUNC: detection of chimerism and contamination in prokaryotic genomes.

Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P

Genome biology, 2021

doi:10.1186/s13059-021-02393-0.