Publications
Preprints
Machine learning inference of natural product chemistry across biosynthetic gene cluster types

Larralde M, Zeller G, biorxiv (2025).

PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity

Larralde M, Zeller G, Carroll LM, biorxiv (2025).

Vigorous exercise associates with the abundance of gut bacterial species reflecting energy pathways: an epidemiological cross-sectional analysis within the Lifelines Dutch Microbiome Project

Morwani J, Ducarmon Q, Zeller G, Deelen J, Beekman M, Slagboom PE, medrxiv (2024).

Long-term fasting remodels gut microbial metabolism and host metabolism

Ducarmon QR, Grundler F, Giannopoulou C, Loume A, Karcher N, Larralde M, Romano SR, [...] Mesnage R, biorXiv (2024).

Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants

Baghai Arassi M, Karcher N, Mastrorilli E, Gross M, Brauer-Nikonow A, Hackett R, Czock D, [...] Zimmermann M, biorXiv (2024).

Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer

Wortmann E, Osswald A, Wylensek D, Kuhls S, Coleman OI, Ducarmon QR, Liang W, [...] Clavel T, biorxiv (2024).

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

Ducarmon QR, Karcher N, Tytgat HLP, Delannoy-Bruno O, Pekel S, Springer F, Schudoma C, Zeller G, biorxiv (2024).

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease

Romano S, Wirbel J, Ansorge R, Schudoma C, Ducarmon QR, Narbad A, Zeller G, bioRxiv (2023).

ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation

Coleman OI, Sorbie A, Bierwith S, Kövilein J, von Stern M, Köhler N, Wirbel J, [...] Haller D, bioRxiv (2023).

Accurate de novo identification of biosynthetic gene clusters with GECCO

Carroll LM, Larralde M, Fleck JS, Ponnudurai R, Milanese A, Cappio E, Zeller G, biorxiv (2021).

2025
Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles

Hohmann M, Iliasov D, Larralde M, Johannes W, Janssen KP, Zeller G, Mascher T, Gulder TAM, ACS Synth Biol (2025).

International consensus statement on microbiome testing in clinical practice

Porcari S, Mullish BH, Asnicar F, Ng SC, Zhao L, Hansen R, O'Toole PW, [...] Ianiro G, Lancet Gastroenterol Hepatol 10 (2) :154-167 (2025).

Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status

Nooij S, Plomp N, Sanders IMJG, Schout L, van der Meulen AE, Terveer EM, Norman JM, [...] Ducarmon QR, Nat Commun 16 (1) :1182 (2025).

2024
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities

Dmitrijeva M, Ruscheweyh HJ, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, [...] Sunagawa S, Nucleic Acids Res (2024).

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies

Wirbel J, Essex M, Forslund SK, Zeller G, Genome Biol 25 (1) :247 (2024).

Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands

Boverhoff D, Kool J, Pijnacker R, Ducarmon QR, Zeller G, Shetty S, Sie S, [...] Fuentes S, Cell Rep 43 (9) :114729 (2024).

Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro

Hohmann M, Brunner V, Johannes W, Schum D, Carroll LM, Liu T, Sasaki D, [...] Gulder TAM, Commun Biol 7 (1) :655 (2024).

2023
High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities

Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, [...] Maier L, Nature Protocols (2023).

Systematic analysis of drug combinations against Gram-positive bacteria

Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, [...] Typas A, Nat Microbiol 8 (11) :2196-2212 (2023).

Remodelling of the intestinal ecosystem during caloric restriction and fasting

Ducarmon QR, Grundler F, Le Maho Y, Wilhelmi de Toledo F, Zeller G, Habold C, Mesnage R, Trends Microbiol 31 (8) :832-844 (2023).

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

Ferretti P, Wirbel J, Maistrenk OM. Van Rossum T, Alves R, Fullam A, Akanni W, Schudoma C, [...] Bork P, Elife (2023).

PyHMMER: a Python library binding to HMMER for efficient sequence analysis

Larralde M, Zeller G, Bioinformatics 39 (5) (2023).

Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data

Sambruni G, Macandog AD, Wirbel J, Cagnina D, Catozzi C, Dallavilla T, Borgo F, [...] Schaefer MH, Genome Med 15 (1) :32 (2023).

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, [...] Mende DR, Nucleic Acids Res 51 (D1) :D760-D766 (2023).

2022
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, [...] Sunagawa S, Microbiome 10 (1) :212 (2022).

Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics

Thomann AK, Wustenberg T, Wirbel J, Knoedler LL, Thomann PA, Zeller G, Ebert MP, [...] Reindl W, BMC Med 20 (1) :366 (2022).

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems

Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, [...] Typas A, Nature 609 (7925) :144-150 (2022).

Biosynthetic potential of the global ocean microbiome

Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, [...] Sunagawa S, Nature 607 (7917) :111-118 (2022).

A faecal microbiota signature with high specificity for pancreatic cancer

Kartal E, Schmidt TSB, Molina-Montes E, Rodriguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, [...] Bork P, Gut 71 (7) :1359-1372 (2022).

Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes

Larralde M, Journal of Open Source Software (2022).

Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, [...] McHardy AC, Nat Methods 19 (4) :429-440 (2022).

Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer

Peuker K, Strigli A, Tauriello DVF, Hendricks A, von Schonfels W, Burmeister G, Brosch M, [...] Zeissig S, Immunity 55 (4) :701-717.e7 (2022).

Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial

Sowah SA, Milanese A, Schubel R, Wirbel J, Kartal E, Johnson TS, Hirche F, [...] Zeller G, Genome Med 14 (1) :30 (2022).

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Velten B, Braunger JM, Argelaguet R, Arnol D, Wirbel J, Bredikhin D, Zeller G, Stegle O, Nat Methods 19 (2) :179-186 (2022).

Association of intraindividual tacrolimus variability with de novo donor-specific HLA antibody development and allograft rejection in pediatric kidney transplant recipients with low immunological risk

Baghai Arassi M, Gauche L, Schmidt J, Höcker B, Rieger S, Süsal C, Tönshoff B, Fichtner A, Pediatric Nephrology 37 (10) :2503-2514 (2022).

2021
Reporting guidelines for human microbiome research: the STORMS checklist

Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, [...] Waldron L, Nat Med 27 (11) :1885-1892 (2021).

Unravelling the collateral damage of antibiotics on gut bacteria

Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Muller P, [...] Typas A, Nature 599 (7883) :120-124 (2021).

Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

Montalban-Arques A, Katkeviciute E, Busenhart P, Bircher A, Wirbel J, Zeller G, Morsy Y, [...] Scharl M, Cell Host Microbe 29 (10) :1573-1588.e7 (2021).

mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities

Ruscheweyh HJ, Milanese A, Paoli L, Sintsova A, Mende DR, Zeller G, Sunagawa S, Curr Protoc 1 (8) :e218 (2021).

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, [...] Zeller G, Genome Biol 22 (1) :93 (2021).

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Blasche S, Kim Y, Mars RAT, Machado D, Maansson M, Kafkia E, Milanese A, [...] Patil KR, Nat Microbiol 6 (2) :196-208 (2021).

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, [...] Claesson MJ, Front Microbiol 12 :635781 (2021).

2020
The gut microbiome in solid organ transplantation

Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B, Pediatr Transplant 24 (7) :e13866 (2020).

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, [...] Segata N, Genome Biol 21 (1) :138 (2020).

Changes in Plasma Short-Chain Fatty Acid Levels after Dietary Weight Loss Among Overweight and Obese Adults over 50 Weeks

Sowah SA, Hirche F, Milanese A, Johnson TS, Grafetstatter M, Schubel R, Kirsten R, [...] Stangl GI, Nutrients 12 (2) (2020).

Metabolic models predict bacterial passengers in colorectal cancer

Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE, Cancer Metab 8 :3 (2020).

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernandez-Plaza A, [...] Bork P, Nucleic Acids Res 48 (D1) :D621-D625 (2020).

2019
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, [...] Sunagawa S, Cell 179 (5) :1068-1083.e21 (2019).

Effects of Weight-Loss Interventions on Short-Chain Fatty Acid Concentrations in Blood and Feces of Adults: A Systematic Review

Sowah SA, Riedl L, Damms-Machado A, Johnson TS, Schubel R, Graf M, Kartal E, [...] Kuhn T, Adv Nutr 10 (4) :673-684 (2019).

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, [...] Zeller G, Nat Med 25 (4) :679-689 (2019).

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, [...] Segata N, Nat Med 25 (4) :667-678 (2019).

Microbial abundance, activity and population genomic profiling with mOTUs2

Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, [...] Sunagawa S, Nat Commun 10 (1) :1014 (2019).

Extensive transmission of microbes along the gastrointestinal tract

Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, [...] Bork P, Elife 8 (2019).

2018
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

Tramontano M, Andrejev S, Pruteanu M, Klunemann M, Kuhn M, Galardini M, Jouhten P, [...] Patil KR, Nat Microbiol 3 (4) :514-522 (2018).

Extensive impact of non-antibiotic drugs on human gut bacteria

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, [...] Typas A, Nature 555 (7698) :623-628 (2018).

Enterotypes in the landscape of gut microbial community composition

Costea PI, Hildebrand F, Arumugam M, Backhed F, Blaser MJ, Bushman FD, de Vos WM, [...] Bork P, Nat Microbiol 3 (1) :8-16 (2018).

2017
Subspecies in the global human gut microbiome

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, [...] Bork P, Mol Syst Biol 13 (12) :960 (2017).

Towards standards for human fecal sample processing in metagenomic studies

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, [...] Bork P, Nat Biotechnol 35 (11) :1069-1076 (2017).

[Microbial Biomarkers for Early Cancer Detection]

Voigt AY, Zeller G, Bork P, Dtsch Med Wochenschr 142 (4) :267-274 (2017).

2016
CART-a chemical annotation retrieval toolkit

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P, Bioinformatics 32 (18) :2869-71 (2016).

MOCAT2: a metagenomic assembly, annotation and profiling framework

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, [...] Bork P, Bioinformatics 32 (16) :2520-3 (2016).

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, [...] Bork P, Science 352 (6285) :586-9 (2016).

Gut Microbiota Linked to Sexual Preference and HIV Infection

Noguera-Julian M, Rocafort M, Guillen Y, Rivera J, Casadella M, Nowak P, Hildebrand F, [...] Paredes R, EBioMedicine 5 :135-46 (2016).

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, [...] Sinha R, PLoS One 11 (5) :e0155362 (2016).

2015
Ocean plankton. Structure and function of the global ocean microbiome

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, [...] Bork P, Science 348 (6237) :1261359 (2015).

Temporal and technical variability of human gut metagenomes

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P, Genome Biol 16 (1) :73 (2015).

2014
Potential of fecal microbiota for early-stage detection of colorectal cancer

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, [...] Bork P, Mol Syst Biol 10 (11) :766 (2014).

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling

van Noort V, Scholch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, [...] Bork P, Cancer Res 74 (20) :5690-9 (2014).

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, [...] Ratsch G, Bioinformatics 30 (9) :1300-1 (2014).

2013
Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, [...] Bork P, Nat Methods 10 (12) :1196-9 (2013).

Accurate and universal delineation of prokaryotic species

Mende DR, Sunagawa S, Zeller G, Bork P, Nat Methods 10 (9) :881-4 (2013).

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, [...] Bork P, Mol Syst Biol 9 :662 (2013).