Deciphering the impact of exposures from the gut microbiome-derived molecular complex in human health and disease

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Publications

Functional prediction of proteins from the human gut archaeome

Auteurs: Polina V Novikova, Susheel Bhanu Busi, Alexander J Probst, Patrick May, Paul Wilmes
Publié dans: ISME Communications, Numéro 4, 2024, ISSN 2730-6151
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/ismeco/ycad014

Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate

Auteurs: Mina Tsenkova, Madita Brauer, Vitaly Igorevich Pozdeev, Marat Kasakin, Susheel Bhanu Busi, Maryse Schmoetten, Dean Cheung, Marianne Meyers, Fabien Rodriguez, Anthoula Gaigneaux, Eric Koncina, Cedric Gilson, Lisa Schlicker, Diran Herebian, Martine Schmitz, Laura de Nies, Ertan Mayatepek, Serge Haan, Carine de Beaufort, Thorsten Cramer, Johannes Meiser, Carole L. Linster, Paul Wilmes, Elisabeth Lete
Publié dans: Nature Communications, Numéro 16, 2025, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-025-56678-0

Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

Auteurs: Dimitrii Pogorelov, Sebastian Felix Nepomuk Bode, Xin He, Javier Ramiro-Garcia, Fanny Hedin, Wim Ammerlaan, Maria Konstantinou, Christophe M. Capelle, Ni Zeng, Aurélie Poli, Olivia Domingues, Guillem Montamat, Oliver Hunewald, Séverine Ciré, Alexandre Baron, Joseph Longworth, Agnieszka Demczuk, Murilo Luiz Bazon, Ingrid Casper, Ludger Klimek, Lorie Neuberger-Castillo, Dominique Revets, Lea Guyo
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-54684-2

Personalized modeling of gut microbiome metabolism throughout the first year of life

Auteurs: Rola Shaaban, Susheel Bhanu Busi, Paul Wilmes, Jean-Louis Guéant, Almut Heinken
Publié dans: Communications Medicine, Numéro 4, 2024, ISSN 2730-664X
Éditeur: Springer Nature
DOI: 10.1038/s43856-024-00715-4

Altered infective competence of the human gut microbiome in COVID-19

Auteurs: Laura de Nies, Valentina Galata, Camille Martin-Gallausiaux, Milena Despotovic, Susheel Bhanu Busi, Chantal J. Snoeck, Lea Delacour, Deepthi Poornima Budagavi, Cedric Christian Laczny, Janine Habier, Paula-Cristina Lupu, Rashi Halder, Joëlle V. Fritz, Taina Marques, Estelle Sandt, Marc Paul O’Sullivan, Soumyabrata Ghosh, Venkata Satagopam, CON-VINCE Consortium, Rejko Krüger, Guy Fagherazzi, Ma
Publié dans: Microbiome, 2023, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-023-01472-7

SARS-CoV-2 transmission in educational settings during an early summer epidemic wave in Luxembourg, 2020

Auteurs: Joël Mossong, Laurent Mombaerts, Lisa Veiber, Jessica Pastore, Gwenaëlle Le Coroller, Michael Schnell, Silvana Masi, Laetitia Huiart, Paul Wilmes
Publié dans: BMC Infectious Diseases, 2021, ISSN 1471-2334
Éditeur: BioMed Central
DOI: 10.1186/s12879-021-06089-5

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Auteurs: Tim Van Den Bossche, Benoit J. Kunath, Kay Schallert, Stephanie S. Schäpe, Paul E. Abraham, Jean Armengaud, Magnus Ø. Arntzen, Ariane Bassignani, Dirk Benndorf, Stephan Fuchs, Richard J. Giannone, Timothy J. Griffin, Live H. Hagen, Rashi Halder, Céline Henry, Robert L. Hettich, Robert Heyer, Pratik Jagtap, Nico Jehmlich, Marlene Jensen, Catherine Juste, Manuel Kleiner, Olivier Langella, Theresa
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients

Auteurs: Christophe M. Capelle, Séverine Ciré, Olivia Domingues, Isabelle Ernens, Fanny Hedin, Aurélie Fischer, Chantal J. Snoeck, Wim Ammerlaan, Maria Konstantinou, Kamil Grzyb, Alexander Skupin, Cara L. Carty, Christiane Hilger, Georges Gilson, Aljosa Celebic, Paul Wilmes, Antonio Del Sol, Ian M. Kaplan, Fay Betsou, Tamir Abdelrahman, Antonio Cosma, Michel Vaillant, Guy Fagherazzi, Markus Ollert, Feng
Publié dans: Cell Reports Medicine, Numéro 3, 2023, Page(s) 100600, ISSN 2666-3791
Éditeur: Elsevier Ltd.
DOI: 10.1016/j.xcrm.2022.100600

Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies

Auteurs: Susana Martínez Arbas, Susheel Bhanu Busi, Pedro Queirós, Laura de Nies, Malte Herold, Patrick May, Paul Wilmes, Emilie E. L. Muller, Shaman Narayanasamy
Publié dans: Frontiers in Genetics, 2021, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2021.666244

Integration of multiple flexible electrodes for real-time detection of barrier formation with spatial resolution in a gut-on-chip system

Auteurs: Mara Lucchetti, Gabriel Werr, Sofia Johansson, Laurent Barbe, Léa Grandmougin, Paul Wilmes, Maria Tenje
Publié dans: Microsystems & Nanoengineering, Numéro 10, 2024, ISSN 2055-7434
Éditeur: Nature Publishing Group
DOI: 10.1038/s41378-023-00640-x

Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome

Auteurs: Matthias Klee, V.T.E. Aho, P. May, A. Heintz-Buschart, Z. Landoulsi, S.R. Jónsdóttir, C. Pauly, L. Pavelka, L. Delacour, A. Kaysen, R. Krüger, P. Wilmes, A.K. Leist, Geeta Acharya, Gloria Aguayo, Myriam Alexandre, Muhammad Ali, Wim Ammerlann, Giuseppe Arena, Michele Bassis, Roxane Batutu, Katy Beaumont, Sibylle Béchet, Guy Berchem, Alexandre Bisdorff, Ibrahim Boussaad, David Bouvier, Lorieza C
Publié dans: The Journal of Prevention of Alzheimer's Disease, Numéro 11, 2025, Page(s) 759-768, ISSN 2274-5807
Éditeur: Elsevier Ltd.
DOI: 10.14283/jpad.2024.19

The gut microbial metabolite formate exacerbates colorectal cancer progression

Auteurs: Dominik Ternes, Mina Tsenkova, Vitaly Igorevich Pozdeev, Marianne Meyers, Eric Koncina, Sura Atatri, Martine Schmitz, Jessica Karta, Maryse Schmoetten, Almut Heinken, Fabien Rodriguez, Catherine Delbrouck, Anthoula Gaigneaux, Aurelien Ginolhac, Tam Thuy Dan Nguyen, Lea Grandmougin, Audrey Frachet-Bour, Camille Martin-Gallausiaux, Maria Pacheco, Lorie Neuberger-Castillo, Paulo Miranda, Nikolaus Zue
Publié dans: Nature Metabolism, Numéro 4, 2023, Page(s) 458-475, ISSN 2522-5812
Éditeur: Springer Nature
DOI: 10.1038/s42255-022-00558-0

SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg

Auteurs: Paul Wilmes, Jacques Zimmer, Jasmin Schulz, Frank Glod, Lisa Veiber, Laurent Mombaerts, Bruno Rodrigues, Atte Aalto, Jessica Pastore, Chantal J. Snoeck, Markus Ollert, Guy Fagherazzi, Joel Mossong, Jorge Goncalves, Alexander Skupin, Ulf Nehrbass
Publié dans: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Éditeur: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100056

Gut microbiome is not associated with mild cognitive impairment in Parkinson’s disease

Auteurs: Velma T. E. Aho, Matthias Klee, Zied Landoulsi, Anna Heintz-Buschart, Lukas Pavelka, Anja K. Leist, Rejko Krüger, Patrick May, Paul Wilmes, null null, Geeta Acharya, Gloria Aguayo, Myriam Alexandre, Muhammad Ali, Wim Ammerlann, Giuseppe Arena, Michele Bassis, Roxane Batutu, Katy Beaumont, Sibylle Béchet, Guy Berchem, Alexandre Bisdorff, Ibrahim Boussaad, David Bouvier, Lorieza Castillo, Gessica
Publié dans: npj Parkinson's Disease, Numéro 10, 2024, ISSN 2373-8057
Éditeur: Nature Publishing Group
DOI: 10.1038/s41531-024-00687-1

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets

Auteurs: Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Publié dans: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbac431

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses

Auteurs: Benoit J. Kunath, Oskar Hickl, Pedro Queirós, Camille Martin-Gallausiaux, Laura A. Lebrun, Rashi Halder, Cedric C. Laczny, Thomas Sebastian B. Schmidt, Matthey R. Hayward, Dörte Becher, Anna Heintz-Buschart, Carine de Beaufort, Peer Bork, Patrick May, Paul Wilmes
Publié dans: Microbiome, 2022, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-022-01435-4

Protocol for a multicentre cross-sectional, longitudinal ambulatory clinical trial in rheumatoid arthritis and Parkinson’s disease patients analysing the relation between the gut microbiome, fasting and immune status in Germany (ExpoBiome)

Auteurs: Bérénice Hansen, Cédric C Laczny, Velma T E Aho, Audrey Frachet-Bour, Janine Habier, Marek Ostaszewski, Andreas Michalsen, Etienne Hanslian, Daniela A Koppold, Anika M Hartmann, Nico Steckhan, Brit Mollenhauer, Sebastian Schade, Kirsten Roomp, Jochen G Schneider, Paul Wilmes
Publié dans: BMJ Open, 2023, ISSN 2044-6055
Éditeur: BMJ Publishing Group
DOI: 10.1136/bmjopen-2022-071380

Metagenomic Profiling of Oral Microbiome Dynamics During Chemoradiotherapy in Head and Neck Squamous Cell Carcinoma Patients

Auteurs: Dominique A. Torozan, Cédric Christian Laczny, Kirsten Roomp, Paul Wilmes, Jochen Fleckenstein, Jochen G. Schneider
Publié dans: Cancer Medicine, Numéro 14, 2025, ISSN 2045-7634
Éditeur: Wiley
DOI: 10.1002/cam4.70589

Bacteroides acidifaciens: Linking dietary fiber to liver health

Auteurs: Viacheslav A. Petrov, Cédric C. Laczny, Paul Wilmes
Publié dans: Cell Metabolism, Numéro 36, 2024, Page(s) 1908-1910, ISSN 1550-4131
Éditeur: Cell Press
DOI: 10.1016/j.cmet.2024.08.002

The benefits, costs and feasibility of a low incidence COVID-19 strategy

Auteurs: Thomas Czypionka, Emil N Iftekhar, Barbara Prainsack, Viola Priesemann, Simon Bauer, André Calero Valdez, Sarah Cuschieri , Enrico Glaab , Eva Grill , Jenny Krutzinna, Christos Lionis, Helena Machado, Carlos Martins, George N Pavlakis, Matjaž Perc, Elena Petelos, Martyn Pickersgill, Alexander Skupin, Eva Schernhammer, Ewa Szczurek, Sotirios Tsiodras, Peter Willeit, Paul Wilmes
Publié dans: The Lancet Regional Health - Europe, 2022, ISSN 2666-7762
Éditeur: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100294

From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders

Auteurs: Aicha Kriaa, Vincent Mariaule, Charlotte De Rudder, Amin Jablaoui, Harry Sokol, Paul Wilmes, Emmanuelle Maguin, Moez Rhimi
Publié dans: Gut Microbes, Numéro 16, 2024, ISSN 1949-0976
Éditeur: Landes Bioscience
DOI: 10.1080/19490976.2024.2333434

Toward hypothesis-driven, personalized microbiome screening

Auteurs: Catherine Sedrani, Paul Wilmes
Publié dans: Cell Reports Methods, 2022, ISSN 2667-2375
Éditeur: Cell Press Elsevier Inc.
DOI: 10.1016/j.crmeth.2021.100139

Mobilome-driven segregation of the resistome in biological wastewater treatment.

Auteurs: Laura de Nies, Susheel Bhanu Busi, Benoit Josef Kunath, Patrick May, Paul Wilmes
Publié dans: eLife, 2022, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.81196

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Auteurs: Tim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau, Paul Wilmes, Robert L. Hettich, Jean Armengaud
Publié dans: Microbiome, 2021, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-021-01176-w

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life

Auteurs: Susheel Bhanu Busi, Laura de Nies, Janine Habier, Linda Wampach, Joëlle V Fritz, Anna Heintz-Buschart, Patrick May, Rashi Halder, Carine de Beaufort, Paul Wilmes
Publié dans: ISME Communications, Numéro 1, 2024, ISSN 2730-6151
Éditeur: Oxford University Press (OUP)
DOI: 10.1038/s43705-021-00003-5

Snapshot: The Expobiome Map

Auteurs: Velma T. E. Aho, Marek Ostaszewski, Camille Martin-Gallausiaux, Cedric C. Laczny, Jochen G. Schneider, Paul Wilmes
Publié dans: Cell Host & Microbe, 2022, ISSN 1931-3128
Éditeur: Cell Press
DOI: 10.1016/j.chom.2022.08.015

Functional meta-omics provide critical insights into long- and short-read assemblies

Auteurs: Valentina Galata, Susheel Bhanu Busi, Benoît Josef Kunath, Laura de Nies, Magdalena Calusinska, Rashi Halder, Patrick May, Paul Wilmes, Cedric Christian Laczny
Publié dans: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbab330

Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson’s disease

Auteurs: Kristopher J. Schmit, Pierre Garcia, Alessia Sciortino, Velma T.E. Aho, Beatriz Pardo Rodriguez, Mélanie H. Thomas, Jean-Jacques Gérardy, Irati Bastero Acha, Rashi Halder, Camille Cialini, Tony Heurtaux, Irina Ostahi, Susheel B. Busi, Léa Grandmougin, Tuesday Lowndes, Yogesh Singh, Eric C. Martens, Michel Mittelbronn, Manuel Buttini, Paul Wilmes
Publié dans: Cell Reports, 2023, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2023.113071

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.

Auteurs: Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz-Buschart, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
Publié dans: Microbiome, 2021, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-020-00993-9

Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes

Auteurs: Zachary L. McAdams, Susheel Bhanu Busi, Kevin L. Gustafson, Nathan Bivens, Craig L. Franklin, Paul Wilmes, Aaron C. Ericsson
Publié dans: Applied Microbiology, Numéro 4, 2025, Page(s) 1600-1615, ISSN 2673-8007
Éditeur: MDPI
DOI: 10.3390/applmicrobiol4040109

The gut microbiome molecular complex in human health and disease

Auteurs: Paul Wilmes, Camille Martin-Gallausiaux, Marek Ostaszewski, Velma T. E. Aho, Polina Novikova, Cedric C. Laczny, Jochen Schneider
Publié dans: Cell Host & Microbe, 2022, ISSN 1931-3128
Éditeur: Cell Press
DOI: 10.1016/j.chom.2022.08.016

Generalisation of COVID-19 incidences provides a biased view of the actual epidemiological situation

Auteurs: Paul Wilmes, Joel Mossong, Thomas G. Dentzer
Publié dans: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Éditeur: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100116

Forecasting the dynamics of a complex microbial community using integrated meta-omics

Auteurs: Francesco Delogu, Benoit J. Kunath, Pedro M. Queirós, Rashi Halder, Laura A. Lebrun, Phillip B. Pope, Patrick May, Stefanie Widder, Emilie E. L. Muller, Paul Wilmes
Publié dans: Nature Ecology & Evolution, 2023, ISSN 2397-334X
Éditeur: Springer Nature
DOI: 10.1038/s41559-023-02241-3

The impact of fasting and caloric restriction on rheumatoid arthritis in humans: A narrative review

Auteurs: Bérénice Hansen, Marta Sánchez-Castro, Lynn Schintgen, Arefeh Khakdan, Jochen G. Schneider, Paul Wilmes
Publié dans: Clinical Nutrition, Numéro 49, 2025, Page(s) 178-186, ISSN 0261-5614
Éditeur: Churchill Livingstone
DOI: 10.1016/j.clnu.2025.04.025

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Auteurs: Catherine Sedrani, Gemma Gomez-Giro, Léa Grandmougin, Jens Christian Schwamborn, Paul Wilmes
Publié dans: JoVE, 2023, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/64483

Studying the Parkinson’s disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study

Auteurs: Begoña Talavera Andújar; Dagny Aurich; Velma T. E. Aho; Randolph R. Singh; Tiejun Cheng; Leonid Zaslavsky; Evan E. Bolton; Brit Mollenhauer; Paul Wilmes; Emma L. Schymanski
Publié dans: Analytical And Bioanalytical Chemistry (1618-2642) (Springer Science and Business Media LLC), 2022-10 , Vol. 414 , N. 25 , P. 7399-7419, 2022, ISSN 1618-2650
Éditeur: Springer Nature
DOI: 10.1007/s00216-022-04207-z

Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere

Auteurs: Indra Banas, Sarah P Esser, Victoria Turzynski, André Soares, Polina Novikova, Patrick May, Cristina Moraru, Mike Hasenberg, Janina Rahlff, Paul Wilmes, Andreas Klingl, Alexander J Probst
Publié dans: The ISME Journal, Numéro 17, 2024, Page(s) 1789-1792, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-023-01474-1

Reservoirs of antimicrobial resistance in the context of One Health

Auteurs: Milena Despotovic, Laura de Nies, Susheel Bhanu Busi, Paul Wilmes
Publié dans: Current Opinion in Microbiology, 2023, ISSN 1369-5274
Éditeur: Elsevier BV
DOI: 10.1016/j.mib.2023.102291

Diversity and biogeography of the bacterial microbiome in glacier-fed streams

Auteurs: Leïla Ezzat, Hannes Peter, Massimo Bourquin, Susheel Bhanu Busi, Grégoire Michoud, Stilianos Fodelianakis, Tyler J. Kohler, Thomas Lamy, Aileen Geers, Paraskevi Pramateftaki, Florian Baier, Ramona Marasco, Daniele Daffonchio, Nicola Deluigi, Paul Wilmes, Michail Styllas, Martina Schön, Matteo Tolosano, Vincent De Staercke, Tom J. Battin
Publié dans: Nature, Numéro 637, 2025, Page(s) 622-630, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-024-08313-z

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment

Auteurs: Laura de Nies, Susheel Bhanu Busi, Mina Tsenkova, Rashi Halder, Elisabeth Letellier, Paul Wilmes
Publié dans: Nature Communications, Numéro 13, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-29919-9

The oral–gut microbiome axis in health and disease

Auteurs: Benoit J. Kunath, Charlotte De Rudder, Cedric C. Laczny, Elisabeth Letellier, Paul Wilmes
Publié dans: Nature Reviews Microbiology, Numéro 22, 2024, Page(s) 791-805, ISSN 1740-1526
Éditeur: Nature Publishing Group
DOI: 10.1038/s41579-024-01075-5

Mantis: flexible and consensus-driven genome annotation

Auteurs: Pedro Queiros, Francesco Delogu, Oskar Hickl, Patrick May, Paul Wilmes
Publié dans: GigaScience, 2021, ISSN 2047-217X
Éditeur: BioMed Central
DOI: 10.1093/gigascience/giab042

Disease Progression, Resilience, and Inflammation Markers During the Coronavirus Disease 2019 Pandemic in Parkinson's Disease.

Auteurs: Claire Pauly, Enrico Glaab, Maxime Hansen , Camille Martin-Gallausiaux, Mirko Ledda, Tainá M. Marques, Paul Wilmes, Rejko Krüger, Nico J. Diederich, NCER-PD Consortium
Publié dans: Movement Disorders, 2022, ISSN 1531-8257
Éditeur: Wiley
DOI: 10.1002/mds.29212

Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

Auteurs: Bianca De Saedeleer, Antoine Malabirade, Javier Ramiro-Garcia, Janine Habier, Jean-Pierre Trezzi, Samantha L. Peters, Annegrät Daujeumont, Rashi Halder, Christian Jäger, Susheel Bhanu Busi, Patrick May, Wolfgang Oertel, Brit Mollenhauer, Cedric C. Laczny, Robert L. Hettich, Paul Wilmes
Publié dans: ISME Communications, 2021, ISSN 2730-6151
Éditeur: Springer Nature
DOI: 10.1038/s43705-021-00078-0

Trajectories of persisting Covid- 19 symptoms up to 24 months after acute infection: findings from the Predi-Covid cohort study

Auteurs: Aurélie Fischer, Lu Zhang, Abir Elbéji, Paul Wilmes, Chantal J. Snoeck, Jérôme Larché, Pauline Oustric, Markus Ollert, Guy Fagherazzi
Publié dans: BMC Infectious Diseases, Numéro 25, 2025, ISSN 1471-2334
Éditeur: BioMed Central
DOI: 10.1186/s12879-025-11023-0

PathoFact: A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

Auteurs: Laura de Nies, Sara Lopes, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
Publié dans: bioRxiv, 2020, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.03.24.006148

Functional assignment of gut-specific archaeal proteins in the human gut microbiome

Auteurs: Polina V. Novikova, Susheel B. Busi, Alexander J. Probst, Patrick May, Paul Wilmes
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.02.01.526569

Metaproteomics in the One Health Framework for Unraveling Microbial Effectors in Microbiomes

Auteurs: Robert Heyer, Maximilian Wolf, Dirk Benndorf, Sergio Uzzau, Jana Seifert, Lucia Grenga, Martin Pabst, Heike Schmitt, Bart Mesuere, Tim Van Den Bossche, Sven-Bastiaan Haange, Nico Jehmlich, Mariagrazia Di Luca, Manuel Ferrer, Sergio Serrano-Villar, Jean Armengaud, Helge Bode, Patrick Hellwig, Catherine Robbe Masselot, Renaud Léonard, Paul Wilmes
Publié dans: ChemRxiv, 2025, ISSN 2573-2293
Éditeur: Cambridge Open Engage
DOI: 10.26434/chemrxiv-2024-jg1mq-v2

Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease

Auteurs: Remy Villette, Júlia Ortís Sunyer, Polina V. Novikova, Velma T. E. Aho, Viacheslav A. Petrov, Oskar Hickl, Susheel Bhanu Busi, Charlotte De Rudder, Benoit Kunath, Anna Heintz-Buschart, Jean-Pierre Trezzi, Rashi Halder, Christian Jäger, Laura A. Lebrun, Annegrät Daujeumont, Sebastian Schade, Annette Janzen, Nico Jehmlich, Martin von Bergen, Cédric C. Laczny, Patrick May, Claudia Trenkwalder, W
Publié dans: bioRxiv, 2025, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.12.13.628341

An archaeal compound as a driver of Parkinson’s disease pathogenesis

Auteurs: Jean-Pierre Trezzi, Velma T. E. Aho, Christian Jäger, Sebastian Schade, Annette Janzen, Oskar Hickl, Benoit Kunath, Mélanie H. Thomas, Kristopher J. Schmit, Pierre Garcia, Alessia Sciortino, Camille Martin-Gallausiaux, Rashi Halder, Oihane Uriarte Huarte, Tony Heurtaux, Ursula Heins-Marroquin, Gemma Gomez-Giro, Katrin Weidenbach, Léa Delacour, Cedric C. Laczny, Polina V. Novikova, Javier Ramiro
Publié dans: Research Square, 2022, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-1827631/v1

UniFuncNet: a flexible network annotation framework

Auteurs: Pedro Queirós, Oskar Hickl, Susana Martínez Arbas, Paul Wilmes, Patrick May
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.03.15.484380

Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson′s disease

Auteurs: Remy Villette, Polina V Novikova, Cedric Christian Laczny, Brit Mollenhauer, Patrick May, Paul Wilmes
Publié dans: bioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.12.18.629142

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets

Auteurs: Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Publié dans: bioRxiv, 2021, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.12.22.473795

The response to ketogenic diet in colorectal cancer is mediated by lasting functional alterations of the gut microbiome

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Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.12.07.570549

Synergistic effect of short- and long-read sequencing on functional meta-omics

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Publié dans: bioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.04.22.440869

Artefactual source of 2-hydroxypyridine

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Publié dans: Research Square, 2023, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-1827631/v2

Trajectories Of Persisting Covid-19 Symptoms Up To 24 Months After Acute Infection: Findings From The Predi-Covid Cohort Study

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Publié dans: ResearchSquare, 2025, ISSN 2693-5015
Éditeur: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-4456228/v1

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

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Publié dans: bioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.12.09.627531

Dietary fibre deprivation and bacterial curli exposure shift gut microbiome and exacerbate Parkinson’s disease-like pathologies in an alpha-synuclein-overexpressing mouse

Auteurs: Kristopher J. Schmit, Alessia Sciortino, Velma T. E. Aho, Pierre Garcia, Beatriz Pardo Rodriguez, Mélanie H. Thomas, Jean-Jacques Gérardy, Rashi Halder, Camille Cialini, Tony Heurtaux, Irati Bastero Acha, Irina Ostahi, Eric C. Martens, Michel Mittelbronn, Manuel Buttini, Paul Wilmes
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.03.21.485143

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): Multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

Auteurs: Alessandro Tanca, Kay Schallert, Lucia Grenga, Samantha L. Peters, Marcello Abbondio, Laura De Diego, Maria Antonietta Deledda, Sven-Bastiaan Haange, Guylaine Miotello, Johan S. Sáenz, Maximilian Wolf, Felipe Bastida, Simon Devos, Guillermina Hernandez-Raquet, Jana Seifert, Paul Wilmes, Tim Van Den Bossche, Benoit J. Kunath, Robert Heyer, Nico Jehmlich, Dirk Benndorf, Robert L. Hettich, Jean Arme
Publié dans: bioRxiv, 2025, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.31.635836

Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy

Auteurs: Feng Hefeng, Dimitrii Pogorelov, Sebastian Bode, Xin He, Javier Ramiro-Garcia, Fanny Hedin, Wim Ammerlaan, Maria Konstantinou, Christophe Capelle, Ni Zeng, Aurélie Poli, Olivia Domingues, Guillem Montamat, Oliver Hunewald, Séverine Cire, Alexandre Baron, Joseph Longworth, Lorie Neuberger-Castillo, Dominique Revets, Léa Guyonnet, Agnieszka Demczuk, Sylvie Delhalle, Jacques Zimmer, Vladimir Benes
Publié dans: Research Square, 2024, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-3917969/v1

Mild cognitive impairment is not associated with gut microbiota alterations in Parkinson’s disease

Auteurs: Velma Aho, Matthias Klee, Zied Landoulsi, Anna Heintz-Buschart, Lukas Pavelka, Anja Leist, Rejko Krüger, Patrick May, Paul Wilmes
Publié dans: Research Square, 2024, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-3372525/v1

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