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

Publicaciones

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

Autores: Laura de Nies, Sara Lopes, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
Publicado en: bioRxiv, 2020, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.03.24.006148

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

Autores: Polina V. Novikova, Susheel B. Busi, Alexander J. Probst, Patrick May, Paul Wilmes
Publicado en: bioRxiv, 2022, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.02.01.526569

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

Autores: 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
Publicado en: Research Square, 2022, ISSN 2693-5015
Editor: Research Square
DOI: 10.21203/rs.3.rs-1827631/v1

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

Autores: Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Publicado en: bioRxiv, 2021, ISSN 2692-8205
Editor: 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

Autores: 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
Publicado en: bioRxiv, 2023, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.12.07.570549

Artefactual source of 2-hydroxypyridine

Autores: 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
Publicado en: Research Square, 2023, ISSN 2693-5015
Editor: 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

Autores: 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
Publicado en: bioRxiv, 2022, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.03.21.485143

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

Autores: 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
Publicado en: Microbiome, 2023, ISSN 2049-2618
Editor: 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

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

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

Autores: 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
Publicado en: Nature Communications, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

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

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

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

Autores: 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
Publicado en: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Editor: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100056

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

Autores: Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart
Publicado en: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Editor: 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

Autores: 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
Publicado en: Microbiome, 2022, ISSN 2049-2618
Editor: 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)

Autores: 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
Publicado en: BMJ Open, 2023, ISSN 2044-6055
Editor: BMJ Publishing Group
DOI: 10.1136/bmjopen-2022-071380

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

Autores: 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
Publicado en: The Lancet Regional Health - Europe, 2022, ISSN 2666-7762
Editor: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100294

Toward hypothesis-driven, personalized microbiome screening

Autores: Catherine Sedrani, Paul Wilmes
Publicado en: Cell Reports Methods, 2022, ISSN 2667-2375
Editor: Cell Press Elsevier Inc.
DOI: 10.1016/j.crmeth.2021.100139

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

Autores: Laura de Nies, Susheel Bhanu Busi, Benoit Josef Kunath, Patrick May, Paul Wilmes
Publicado en: eLife, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.81196

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

Autores: 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
Publicado en: Microbiome, 2021, ISSN 2049-2618
Editor: Springer Nature
DOI: 10.1186/s40168-021-01176-w

Snapshot: The Expobiome Map

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

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

Autores: Valentina Galata, Susheel Bhanu Busi, Benoît Josef Kunath, Laura de Nies, Magdalena Calusinska, Rashi Halder, Patrick May, Paul Wilmes, Cedric Christian Laczny
Publicado en: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Editor: 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

Autores: 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
Publicado en: Cell Reports, 2023, ISSN 2211-1247
Editor: 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.

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

The gut microbiome molecular complex in human health and disease

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

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

Autores: Paul Wilmes, Joel Mossong, Thomas G. Dentzer
Publicado en: The Lancet Regional Health - Europe, 2021, ISSN 2666-7762
Editor: Elsevier Ltd.
DOI: 10.1016/j.lanepe.2021.100116

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

Autores: 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
Publicado en: Nature Ecology & Evolution, 2023, ISSN 2397-334X
Editor: Springer Nature
DOI: 10.1038/s41559-023-02241-3

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

Autores: Catherine Sedrani, Gemma Gomez-Giro, Léa Grandmougin, Jens Christian Schwamborn, Paul Wilmes
Publicado en: JoVE, 2023, ISSN 1940-087X
Editor: 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

Autores: 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
Publicado en: 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
Editor: Springer Nature
DOI: 10.1007/s00216-022-04207-z

Reservoirs of antimicrobial resistance in the context of One Health

Autores: Milena Despotovic, Laura de Nies, Susheel Bhanu Busi, Paul Wilmes
Publicado en: Current Opinion in Microbiology, 2023, ISSN 1369-5274
Editor: Elsevier BV
DOI: 10.1016/j.mib.2023.102291

Mantis: flexible and consensus-driven genome annotation

Autores: Pedro Queiros, Francesco Delogu, Oskar Hickl, Patrick May, Paul Wilmes
Publicado en: GigaScience, 2021, ISSN 2047-217X
Editor: BioMed Central
DOI: 10.1093/gigascience/giab042

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

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

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

Autores: 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
Publicado en: ISME Communications, 2021, ISSN 2730-6151
Editor: Springer Nature
DOI: 10.1038/s43705-021-00078-0

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