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, Karcher N, Larralde MF, Vossen RHAM, Kloet SL, Faber KN, Harmsen HJM, Zeller GF, Kuijper EJ, Smits WK, Ducarmon QR.

Nat Commun, 2025

doi:10.1038/s41467-025-56449-x.

Metagenomic global survey and in-depth genomic analyses ofRuminococcus gnavusreveal differences across host lifestyle and health status

Nooij S, Plomp N, Sanders I, Schout L, van der Meulen A, Terveer E, Norman J, Karcher N, Larralde M, Vossen R, Kloet S, Faber K, Harmsen H, Zeller G, Kuijper E, Smits W, Ducarmon Q.

2024

doi:10.1101/2024.06.27.600998.

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, Tönshoff B, Zeller G, Zimmermann M.

2024

doi:10.1101/2024.03.28.586928.

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 Res, 2023

doi:10.1093/nar/gkac1078.

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.

Ianiro G, Punčochář M, Karcher N, Porcari S, Armanini F, Asnicar F, Beghini F, Blanco-Míguez A, Cumbo F, Manghi P, Pinto F, Pinto F, Masucci L, Quaranta G, De Giorgi S, Sciumè GD, Bibbò S, Del Chierico F, Putignani L, Sanguinetti M, Gasbarrini A, Valles-Colomer M, Cammarota G, Segata N.

Nat Med, 2022

doi:10.1038/s41591-022-01964-3.

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, Sunagawa S, Zeller G.

Genome Biol, 2021

doi:10.1186/s13059-021-02306-1.

The gut microbiome in solid organ transplantation.

Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B.

Pediatr Transplant, 2020

doi:10.1111/petr.13866.

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, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N.

Genome Biol, 2020

doi:10.1186/s13059-020-02042-y.

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, Sunagawa S, Zeller G.

2020

doi:10.1101/2020.02.06.931808.

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species.

Manara S, Asnicar F, Beghini F, Bazzani D, Cumbo F, Zolfo M, Nigro E, Karcher N, Manghi P, Metzger MI, Pasolli E, Segata N.

Genome Biol, 2019

doi:10.1186/s13059-019-1923-9.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N.

Cell Host Microbe, 2019

doi:10.1016/j.chom.2019.08.018.

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, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.

Nat Med, 2019

doi:10.1038/s41591-019-0405-7.

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N.

Cell, 2019

doi:10.1016/j.cell.2019.01.001.