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

Project Information

ExpoBiome

Grant agreement ID: 863664

DOI 10.3030/863664

EC signature date 17 February 2020

Start date 1 November 2020

End date 31 October 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 998 620,00

EU contribution € 1 998 620,00

Coordinated by

UNIVERSITE DU LUXEMBOURG
Luxembourg

Publications

Non-peer reviewed articles (7)

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

Author(s): Laura de Nies, Sara Lopes, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
Published in: bioRxiv, 2020, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.03.24.006148

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

Author(s): Polina V. Novikova, Susheel B. Busi, Alexander J. Probst, Patrick May, Paul Wilmes
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.02.01.526569

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

Author(s): 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
Published in: Research Square, 2022, ISSN 2693-5015
Publisher: Research Square
DOI: 10.21203/rs.3.rs-1827631/v1

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

Author(s): Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Published in: bioRxiv, 2021, ISSN 2692-8205
Publisher: 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

Author(s): Mina Tsenkova, Madita Brauer, Marat Kasakin, Susheel Bhanu Busi, Maryse Schmoetten, Anthoula Gaigneaux, Vitaly Pozdeev, Marianne Meyers, Eric Koncina, Diran Herebian, Fabien Rodriguez, Martine Schmitz, Laura de Nies, Ertan Mayatepek, Serge Haan, Carine de Beaufort, Jérôme Graas, Thorsten Cramer, Carole Linster, Paul Wilmes, Elisabeth Letellier
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.12.07.570549

Artefactual source of 2-hydroxypyridine

Author(s): Velma T. E. Aho, Jean-Pierre Trezzi, 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, Cédric C. Laczny, Polina V. Novikova, Javier Ramir
Published in: Research Square, 2023, ISSN 2693-5015
Publisher: Research Square
DOI: 10.21203/rs.3.rs-1827631/v2

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

Author(s): 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
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.03.21.485143

Peer reviewed articles (25)

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

Author(s): 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
Published in: Microbiome, 2023, ISSN 2049-2618
Publisher: 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

Author(s): Joël Mossong, Laurent Mombaerts, Lisa Veiber, Jessica Pastore, Gwenaëlle Le Coroller, Michael Schnell, Silvana Masi, Laetitia Huiart, Paul Wilmes
Published in: BMC Infectious Diseases, 2021, ISSN 1471-2334
Publisher: BioMed Central
DOI: 10.1186/s12879-021-06089-5

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

Author(s): 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
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

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

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

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

Author(s): 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
Published in: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Publisher: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100056

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

Author(s): Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Published in: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Publisher: 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

Author(s): 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
Published in: Microbiome, 2022, ISSN 2049-2618
Publisher: 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)

Author(s): 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
Published in: BMJ Open, 2023, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2022-071380

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

Author(s): 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
Published in: The Lancet Regional Health - Europe, 2022, ISSN 2666-7762
Publisher: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100294

Toward hypothesis-driven, personalized microbiome screening

Author(s): Catherine Sedrani, Paul Wilmes
Published in: Cell Reports Methods, 2022, ISSN 2667-2375
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.crmeth.2021.100139

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

Author(s): Laura de Nies, Susheel Bhanu Busi, Benoit Josef Kunath, Patrick May, Paul Wilmes
Published in: eLife, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.81196

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

Author(s): 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
Published in: Microbiome, 2021, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-021-01176-w

Snapshot: The Expobiome Map 

Author(s): Velma T. E. Aho, Marek Ostaszewski, Camille Martin-Gallausiaux, Cedric C. Laczny, Jochen G. Schneider, Paul Wilmes
Published in: Cell Host & Microbe, 2022, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2022.08.015

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

Author(s): Valentina Galata, Susheel Bhanu Busi, Benoît Josef Kunath, Laura de Nies, Magdalena Calusinska, Rashi Halder, Patrick May, Paul Wilmes, Cedric Christian Laczny
Published in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Publisher: 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

Author(s): 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
Published in: Cell Reports, 2023, ISSN 2211-1247
Publisher: 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.

Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz-Buschart, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
Published in: Microbiome, 2021, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-020-00993-9

The gut microbiome molecular complex in human health and disease

Author(s): Paul Wilmes, Camille Martin-Gallausiaux, Marek Ostaszewski, Velma T. E. Aho, Polina Novikova, Cedric C. Laczny, Jochen Schneider
Published in: Cell Host & Microbe, 2022, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2022.08.016

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

Author(s): Paul Wilmes, Joel Mossong, Thomas G. Dentzer
Published in: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Publisher: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100116

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

Author(s): 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
Published in: Nature Ecology & Evolution, 2023, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-023-02241-3

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

Author(s): Catherine Sedrani, Gemma Gomez-Giro, Léa Grandmougin, Jens Christian Schwamborn, Paul Wilmes
Published in: JoVE, 2023, ISSN 1940-087X
Publisher: 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

Author(s): 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
Published in: 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
Publisher: Springer Nature
DOI: 10.1007/s00216-022-04207-z

Reservoirs of antimicrobial resistance in the context of One Health

Author(s): Milena Despotovic, Laura de Nies, Susheel Bhanu Busi, Paul Wilmes
Published in: Current Opinion in Microbiology, 2023, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2023.102291

Mantis: flexible and consensus-driven genome annotation

Author(s): Pedro Queiros, Francesco Delogu, Oskar Hickl, Patrick May, Paul Wilmes
Published in: GigaScience, 2021, ISSN 2047-217X
Publisher: BioMed Central
DOI: 10.1093/gigascience/giab042

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

Author(s): Claire Pauly, Enrico Glaab, Maxime Hansen , Camille Martin-Gallausiaux, Mirko Ledda, Tainá M. Marques, Paul Wilmes, Rejko Krüger, Nico J. Diederich, NCER-PD Consortium
Published in: Movement Disorders, 2022, ISSN 1531-8257
Publisher: Wiley
DOI: 10.1002/mds.29212

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

Author(s): 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
Published in: ISME Communications, 2021, ISSN 2730-6151
Publisher: Springer Nature
DOI: 10.1038/s43705-021-00078-0