Gut OncoMicrobiome Signatures (GOMS) associated with cancer incidence, prognosis and prediction of treatment response.

Project Information

ONCOBIOME

Grant agreement ID: 825410

DOI

10.3030/825410

Project closed

EC signature date 3 December 2018

Start date 1 January 2019

End date 30 June 2025

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost

€ 15 041 511,25

EU contribution

€ 14 994 551,25

Coordinated by

INSTITUT GUSTAVE ROUSSY
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Other (5)

Identification of commensals from GOMS associated with toxicity effects
Transcriptomics landscape

Transcriptomics landscape in dedicated cohorts (GEPAR-TREIZE, PARTNER, PBCP, ONCOBIOTICS, NIRVANA, CHECK’UP)

"Creating the notion of ""Drugging GOMS or GOMSING drugs"""
Identification of commensals from GOMS associated with pro- or anticancer effects
Genomic landscape

Genomic landscape of most of CRC and BC cohorts using a standardized methodology

Documents, reports (15)

Communication plan and website
Freeze of the statistical and machine learning tools

Freeze of the statistical and machine learning tools.

Immunoscore on most of ONCOBIOME cohorts

Immunoscore on most of ONCOBIOME cohorts using a standardized methodology

Completion of running the metagenomics protocols

Completion of running the metagenomics protocols on all the samples included in the project

Epidemiological analysis

Epidemiological analysis of main flaws in data interpretation

Discovery of commensal-specific regulatory properties

Discovery of commensalspecific regulatory properties on immune cell migration

Banking, sequencing and functional description of new commensals

Banking sequencing and functional description of new commensals

Metabolomics on plasma

Metabolomics on plasma in dedicated cohorts

Preliminary dietary data

Preliminary dietary data from existing cohorts where available

Standardization of shotgun microbiome analysis

A detailed technical description of standardization of shotgun microbiome analysis on the unified database

Tumor mutational burden

Tumor mutational burden and PDL1 for dedicated cohorts

Discovery of commensal-specific metabolites

Discovery of commensal one or severalspecific metabolites

Freeze of the database of the profiles

Freeze of the database of the profiles from all the metagenomes of the project obtained with the tools of D22

Culturomics of E. hirae

Culturomics of E hirae for most cohorts amenable to ICBs

Completion of the curatedCancerMetagenomicData resource

Websites, patent fillings, videos etc. (1)

ONCOBIOME logo and graphic chart

Publications

Peer reviewed articles (59)

Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai

Author(s): Liviana Ricci, Marta Selma-Royo, Davide Golzato, Charlotte Servais, Amir Nabinejad, Paolo Marchi, Michal Punčochář, Francesco Trenti, Mar Garcia-Aloy, Federica Armanini, Roberta Marconi, Francesco Asnicar, Federica Pinto, Graziano Guella, Sabrina Tamburini, Nicola Segata
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 75, 2025, ISSN 1466-5026
Publisher: Society for General Microbiology
DOI: 10.1099/ijsem.0.006798

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Author(s): Elisa Piperni, Long H. Nguyen, Paolo Manghi, Hanseul Kim, Edoardo Pasolli, Sergio Andreu-Sánchez, Alberto Arrè, Kate M. Bermingham, Aitor Blanco-Míguez, Serena Manara, Mireia Valles-Colomer, Elco Bakker, Fabio Busonero, Richard Davies, Edoardo Fiorillo, Francesca Giordano, George Hadjigeorgiou, Emily R. Leeming, Monia Lobina, Marco Masala, Andrea Maschio, Lauren J. McIver, Mauro Pala, Maristell
Published in: Cell, Issue 187, 2025, Page(s) 4554-4570.e18, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2024.06.018

Gut microbiota composition in colorectal cancer patients is genetically regulated

Author(s): Francesca Colombo, Oscar Illescas, Sara Noci, Francesca Minnai, Giulia Pintarelli, Angela Pettinicchio, Alberto Vannelli, Luca Sorrentino, Luigi Battaglia, Maurizio Cosimelli, Tommaso A. Dragani & Manuela Gariboldi
Published in: Scientific Reports, Issue 12, 2022, Page(s) 11424, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-15230-6

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

Author(s): Gianluca Ianiro, Michal Punčochář, Nicolai Karcher, Serena Porcari, Federica Armanini, Francesco Asnicar, Francesco Beghini, Aitor Blanco-Míguez, Fabio Cumbo, Paolo Manghi, Federica Pinto, Luca Masucci, Gianluca Quaranta, Silvia De Giorgi, Giusi Desirè Sciumè, Stefano Bibbò, Federica Del Chierico, Lorenza Putignani, Maurizio Sanguinetti, Antonio Gasbarrini, Mireia Valles-Colomer, Giovanni C
Published in: Nature Medicine, 2022, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-01964-3

A Fecal MicroRNA Signature by Small RNA Sequencing Accurately Distinguishes Colorectal Cancers: Results From a Multicenter Study

Author(s): Barbara Pardini, Giulio Ferrero, Sonia Tarallo, Gaetano Gallo, Antonio Francavilla, Nicola Licheri, Mario Trompetto, Giuseppe Clerico, Carlo Senore, Sergio Peyre, Veronika Vymetalkova, Ludmila Vodickova, Vaclav Liska, Ondrej Vycital, Miroslav Levy, Peter Macinga, Tomas Hucl, Eva Budinska, Pavel Vodicka, Francesca Cordero, Alessio Naccarati
Published in: Gastroenterology, Issue 165, 2023, Page(s) 582-599.e8, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2023.05.037

Using empirical biological knowledge to infer regulatory networks from multi-omics data

Author(s): Pačínková A., Popovici V.
Published in: BMC Bioinformatics, Issue 23, 2022, Page(s) 351, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04891-9

Bile acids regulate MAdCAM-1 expression to link the gut microbiota to cancer immunosurveillance

Author(s): Marine Fidelle, Ai-Ling Tian, Laurence Zitvogel, Guido Kroemer
Published in: OncoImmunology, Issue 12, 2024, ISSN 2162-4011
Publisher: Landes Bioscience
DOI: 10.1080/2162402x.2023.2224672

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in advanced non-small cell lung cancer patients

Author(s): Lisa Derosa, Bertrand Routy, Andrew Maltez Thomas, Valerio Iebba, Gerard Zalcman, Sylvie Friard, Julien Mazieres, Clarisse Audigier-Valette, Denis Moro-Sibilot, François Goldwasser, Carolina Alves Costa Silva, Safae Terrisse, Melodie Bonvalet, Arnaud Scherpereel, Hervé Pegliasco, Corentin Richard, François Ghiringhelli, Arielle Elkrief, Antoine Desilets, Felix Blanc-Durand, Fabio Cumbo, Aitor B
Published in: Nature Medicine, Issue 28, 2022, Page(s) 315-324, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01655-5

Blue poo: impact of gut transit time on the gut microbiome using a novel marker.

Author(s): Francesco Asnicar; Emily R Leeming; Eirini Dimidi; Mohsen Mazidi; Paul W. Franks; Haya Al Khatib; Ana M. Valdes; Richard Davies; Elco Bakker; Lucy Francis; Andrew T. Chan; Rachel J. Gibson; George Hadjigeorgiou; Jonathan Wolf; Tim D. Spector; Nicola Segata; Sarah Berry
Published in: Gut, Issue 7, 2021, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-323877

AI-based classification of anticancer drugs reveals nucleolar condensation as a predictor of immunogenicity

Author(s): Giulia Cerrato, Peng Liu, Liwei Zhao, Adriana Petrazzuolo, Juliette Humeau, Sophie Theresa Schmid, Mahmoud Abdellatif, Allan Sauvat, Guido Kroemer
Published in: Molecular Cancer, Issue 23, 2024, ISSN 1476-4598
Publisher: BioMed Central
DOI: 10.1186/s12943-024-02189-3

Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma

Author(s): Johannes R. Björk, Laura A. Bolte, Andrew Maltez Thomas, Karla A. Lee, Niccolo Rossi, Thijs T. Wind, Lotte M. Smit, Federica Armanini, Francesco Asnicar, Aitor Blanco-Miguez, Ruth Board, Neus Calbet-Llopart, Lisa Derosa, Nathalie Dhomen, Kelly Brooks, Mark Harland, Mark Harries, Paul Lorigan, Paolo Manghi, Richard Marais, Julia Newton-Bishop, Luigi Nezi, Federica Pinto, Miriam Potrony, Susana Pui
Published in: Nature Medicine, Issue 30, 2024, Page(s) 785-796, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-024-02803-3

Gut Microbiota Modulation through <i>Akkermansia</i> spp<i>.</i> Supplementation Increases CAR T-cell Potency

Author(s): Laura Marcos-Kovandzic, Michele Avagliano, Myriam Ben Khelil, Janesa Srikanthan, Rim Abdallah, Valentina Petrocelli, Jessica Rengassamy, Alexia Alfaro, Mathilde Bied, Marine Fidelle, Gladys Ferrere, Romain Daillère, Ahmadreza Arbab, Roula Amine-Hneineh, Arnaud Pages, Peggy Dartigues, Pierre Ly, Sylvain Simon, Sylvère Durand, Adrian Gottschlich, Florent Ginhoux, Camille Blériot, Peng Liu, Liwei
Published in: Cancer Discovery, 2025, Page(s) OF1-OF22, ISSN 2159-8274
Publisher: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-24-1230

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome

Author(s): Lisa Derosa, Valerio Iebba, Carolina Alves Costa Silva, Gianmarco Piccinno, Guojun Wu, Leonardo Lordello, Bertrand Routy, Naisi Zhao, Cassandra Thelemaque, Roxanne Birebent, Federica Marmorino, Marine Fidelle, Meriem Messaoudene, Andrew Maltez Thomas, Gerard Zalcman, Sylvie Friard, Julien Mazieres, Clarisse Audigier-Valette, Denis Moro- Sibilot, François Goldwasser, Arnaud Scherpereel, Hervé Peg
Published in: Cell, Issue 187, 2024, Page(s) 3373-3389.e16, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2024.05.029

Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis

Author(s): Floor S. Baas, Nele Brusselaers, Iris D. Nagtegaal, Lars Engstrand, Annemarie Boleij
Published in: Cell Host &amp; Microbe, Issue 32, 2025, Page(s) 1235-1247, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2024.07.008

A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers

Author(s): Marine Fidelle, Conrad Rauber, Carolina Alves Costa Silva, Ai-Ling Tian, Imran Lahmar, Anne-Laure Mallard de La Varende, Liwei Zhao, Cassandra Thelemaque, Isabelle Lebhar, Meriem Messaoudene, Eugenie Pizzato, Roxanne Birebent, Maxime Descartes Mbogning Fonkou, Silvia Zoppi, Anna Reni, Cécile Dalban, Marion Leduc, Gladys Ferrere, Sylvère Durand, Pierre Ly, Aymeric Silvin, Kevin Mulder, Charles-An
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abo2296

Intake of Natural Compounds and Circulating microRNA Expression Levels: Their Relationship Investigated in Healthy Subjects With Different Dietary Habits.

Author(s): Ferrero G, Carpi S, Polini B, Pardini B, Nieri P, Impeduglia A, Grioni S, Tarallo S, Naccarati A.
Published in: Frontiers in pharmacology., 2021, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2020.619200

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3

Author(s): Francesco Beghini; Lauren J. McIver; Aitor Blanco-Míguez; Leonard Dubois; Francesco Asnicar; Sagun Maharjan; Sagun Maharjan; Ana Mailyan; Ana Mailyan; Paolo Manghi; Matthias Scholz; Andrew Maltez Thomas; Mireia Valles-Colomer; George Weingart; George Weingart; Yancong Zhang; Yancong Zhang; Moreno Zolfo; Curtis Huttenhower; Curtis Huttenhower; Eric A. Franzosa; Eric A. Franzosa; Nicola Segata; Nic
Published in: eLife, Issue 2, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.65088

Modulation of faecal miRNAs highlights the preventive effects of a Mediterranean low-inflammatory dietary intervention

Author(s): Oscar Illescas, Giulio Ferrero, Antonino Belfiore, Barbara Pardini, Sonia Tarallo, Chiara M. Ciniselli, Sara Noci, Elena Daveri, Stefano Signoroni, Laura Cattaneo, Andrea Mancini, Daniele Morelli, Massimo Milione, Francesca Cordero, Licia Rivoltini, Paolo Verderio, Patrizia Pasanisi, Marco Vitellaro, Alessio Naccarati, Manuela Gariboldi
Published in: Clinical Nutrition, Issue 43, 2024, Page(s) 951-959, ISSN 0261-5614
Publisher: Churchill Livingstone
DOI: 10.1016/j.clnu.2024.02.023

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Author(s): Francesco Asnicar, Sarah E. Berry, Ana M. Valdes, Long H. Nguyen, Gianmarco Piccinno, David A. Drew, Emily Leeming, Rachel Gibson, Caroline Le Roy, Haya Al Khatib, Lucy Francis, Mohsen Mazidi, Olatz Mompeo, Mireia Valles-Colomer, Adrian Tett, Francesco Beghini, Léonard Dubois, Davide Bazzani, Andrew Maltez Thomas, Chloe Mirzayi, Asya Khleborodova, Sehyun Oh, Rachel Hine, Christopher Bonnett, Joan
Published in: Nature Medicine, 2021, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-020-01183-8

The 8q24 region hosts miRNAs altered in biospecimens of colorectal and bladder cancer patients

Author(s): Amedeo Gagliardi, Giulia Francescato, Giulio Ferrero, Giovanni Birolo, Sonia Tarallo, Antonio Francavilla, Giulia Piaggeschi, Carla Di Battista, Gaetano Gallo, Alberto Realis Luc, Carlotta Sacerdote, Giuseppe Matullo, Paolo Vineis, Alessio Naccarati, Barbara Pardini
Published in: Cancer Medicine, Issue 00, 2022, Page(s) 1-15, ISSN 2045-7634
Publisher: John Wiley & Sons Ltd
DOI: 10.1002/cam4.5375

Faecal miRNA profiles associated with age, sex, BMI, and lifestyle habits in healthy individuals.

Author(s): Antonio Francavilla; Amedeo Gagliardi; Giulia Piaggeschi; Sonia Tarallo; Francesca Cordero; Ruggero G. Pensa; Alessia Impeduglia; Gian Paolo Caviglia; Davide Giuseppe Ribaldone; Gaetano Gallo; Sara Grioni; Giulio Ferrero; Barbara Pardini; Alessio Naccarati
Published in: Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021), Issue 2, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-00014-1

Benzodiazepines compromise the outcome of cancer immunotherapy

Author(s): Léa Montégut, Lisa Derosa, Meriem Messaoudene, Hui Chen, Flavia Lambertucci, Bertrand Routy, Laurence Zitvogel, Isabelle Martins, Guido Kroemer
Published in: OncoImmunology, Issue 13, 2024, ISSN 2162-402X
Publisher: Informa UK Limited
DOI: 10.1080/2162402x.2024.2413719

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

Author(s): Karcher, N.; Pasolli, E.; Asnicar, F.; Huang, K. D.; Huang, K. D.; Tett, A.; Manara, S.; Armanini, F.; Bain, D.; Duncan, S. H.; Louis, P.; Zolfo, M.; Manghi, P.; Valles-Colomer, M.; Raffaeta, R.; Rota-Stabelli, O.; Collado, M. C.; Zeller, G.; Falush, D.; Maixner, F.; Walker, A. W.; Huttenhower, C.; Huttenhower, C.; Segata, N.
Published in: Genome Biology, Issue 9, 2020, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02042-y

Profiling small RNAs in fecal immunochemical tests: is it possible?

Author(s): Einar Birkeland, Giulio Ferrero, Barbara Pardini, Sinan U. Umu, Sonia Tarallo, Sara Bulfamante, Geir Hoff, Carlo Senore, Trine B Rounge, Alessio Naccarati
Published in: Molecular Cancer, Issue 22, 2023, ISSN 1476-4598
Publisher: BioMed Central
DOI: 10.1186/s12943-023-01869-w

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system

Author(s): Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero
Published in: Bioinformatics, Issue 39(5):btad201, 2024, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/2022.08.08.503120

Multiple regulatory events contribute to a widespread circular RNA downregulation in precancer and early stage of colorectal cancer development

Author(s): Alessandro Camandona, Amedeo Gagliardi, Nicola Licheri, Sonia Tarallo, Giulia Francescato, Eva Budinska, Martina Carnogurska, Barbora Zwinsová, Barbara Martinoglio, Lorenzo Franchitti, Gaetano Gallo, Santina Cutrupi, Michele De Bortoli, Barbara Pardini, Alessio Naccarati, Giulio Ferrero
Published in: Biomarker Research, Issue 13, 2025, ISSN 2050-7771
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s40364-025-00744-8

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals.

Author(s): Sonia Tarallo; Giulio Ferrero; Francesca De Filippis; Antonio Francavilla; Edoardo Pasolli; Valentina Panero; Francesca Cordero; Nicola Segata; Sara Grioni; Ruggero G. Pensa; Barbara Pardini; Danilo Ercolini; Alessio Naccarati
Published in: Gut, Issue 1, 2021, ISSN 1468-3288
Publisher: BMJ
DOI: 10.1136/gutjnl-2021-325168

SnoRNA profiling in colorectal cancer and assessment of non-invasive biomarker capacity by ddPCR in fecal samples

Author(s): Javier Gómez-Matas, Saray Duran-Sanchon, Juan-José Lozano, Giulio Ferrero, Sonia Tarallo, Barbara Pardini, Alessio Naccarati, Antoni Castells, Meritxell Gironella
Published in: iScience, Issue 27, 2024, Page(s) 109283, ISSN 2589-0042
Publisher: Cell press
DOI: 10.1016/j.isci.2024.109283

At the forefront of the sequencing revolution—notes from the RNGS19 conference

Author(s): Sander Wuyts, Nicola Segata
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-019-1714-3

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

Author(s): Adrian Tett, Kun D. Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, Maria Carmen Collado, Dan R. Littman, Daniel Eibach, Danilo Ercolini, Omar Ro
Published in: Cell Host & Microbe, Issue 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2019.08.018

Multiple levels of the unknown in microbiome research

Author(s): Andrew Maltez Thomas, Nicola Segata
Published in: BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0667-z

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples

Author(s): Sonia Tarallo, Giulio Ferrero, Gaetano Gallo, Antonio Francavilla, Giuseppe Clerico, Alberto Realis Luc, Paolo Manghi, Andrew Maltez Thomas, Paolo Vineis, Nicola Segata, Barbara Pardini, Alessio Naccarati, Francesca Cordero
Published in: mSystems, Issue 4/5, 2019, ISSN 2379-5077
Publisher: American Society for Microbiology Journals
DOI: 10.1128/mSystems.00289-19

Detecting contamination in viromes using ViromeQC

Author(s): Moreno Zolfo, Federica Pinto, Francesco Asnicar, Paolo Manghi, Adrian Tett, Frederic D. Bushman, Nicola Segata
Published in: Nature Biotechnology, Issue 37/12, 2019, Page(s) 1408-1412, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-019-0334-5

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Author(s): Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, Nicola Segata
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16366-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Author(s): Nicolai Karcher; Eleonora Nigro; Michal Punčochář; Aitor Blanco-Míguez; Matteo Ciciani; Paolo Manghi; Moreno Zolfo; Fabio Cumbo; Serena Manara; Davide Golzato; Anna Cereseto; Manimozhiyan Arumugam; Thi Phuong Nam Bui; Hanne L. P. Tytgat; Hanne L. P. Tytgat; Mireia Valles-Colomer; Willem M. de Vos; Willem M. de Vos; Nicola Segata; Nicola Segata
Published in: Genome Biology, Issue 4, 2021, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-021-02427-7

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial

Author(s): Bertrand Routy, John G. Lenehan, Wilson H. Miller, Rahima Jamal, Meriem Messaoudene, Brendan A. Daisley, Cecilia Hes, Kait F. Al, Laura Martinez-Gili, Michal Punčochář, Scott Ernst, Diane Logan, Karl Belanger, Khashayar Esfahani, Corentin Richard, Marina Ninkov, Gianmarco Piccinno, Federica Armanini, Federica Pinto, Mithunah Krishnamoorthy, Rene Figueredo, Pamela Thebault, Panteleimon Takis, Ja
Published in: Nature Medicine, Issue 29, 2023, Page(s) 2121-2132, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-023-02453-x

Long-distance microbial mechanisms impacting cancer immunosurveillance

Author(s): Laurence Zitvogel, Marine Fidelle, Guido Kroemer
Published in: Immunity, Issue 57, 2025, Page(s) 2013-2029, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2024.07.020

Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

Author(s): Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, F
Published in: Nature Biotechnology, 2023, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01688-w

Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy

Author(s): Andrew Maltez Thomas, Marine Fidelle, Bertrand Routy, Guido Kroemer, Jennifer A. Wargo, Nicola Segata, Laurence Zitvogel
Published in: Nature Reviews Clinical Oncology, Issue 20, 2023, Page(s) 583-603, ISSN 1759-4774
Publisher: Nature Publishing Group
DOI: 10.1038/s41571-023-00785-8

Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial

Author(s): Carolina Alves Costa Silva, Gianmarco Piccinno, Déborah Suissa, Mélanie Bourgin, Gerty Schreibelt, Sylvère Durand, Roxanne Birebent, Marine Fidelle, Cissé Sow, Fanny Aprahamian, Paolo Manghi, Michal Punčochář, Francesco Asnicar, Federica Pinto, Federica Armanini, Safae Terrisse, Bertrand Routy, Damien Drubay, Alexander M. M. Eggermont, Guido Kroemer, Nicola Segata, Laurence Zitvogel, Lisa D
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45357-1

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

Author(s): Karla A. Lee, Andrew Maltez Thomas, Laura A. Bolte, Johannes R. Björk, Laura Kist de Ruijter, Federica Armanini, Francesco Asnicar, Aitor Blanco-Miguez, Ruth Board, Neus Calbet-Llopart, Lisa Derosa, Nathalie Dhomen, Kelly Brooks, Mark Harland, Mark Harries, Emily R. Leeming, Paul Lorigan, Paolo Manghi, Richard Marais, Julia Newton-Bishop, Luigi Nezi, Federica Pinto, Miriam Potrony, Susana Puig, P
Published in: Nature Medicine, Issue 28, 2022, Page(s) 535-544, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-01695-5

Prevotella diversity, niches and interactions with the human host

Author(s): Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini, Nicola Segata
Published in: Nature reviews. Microbiology, 2021, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-021-00559-y

Fecal miRNA profiles in colorectal cancers with mucinous morphology

Author(s): Alessio Naccarati, Mihnea P Dragomir, Sonia Tarallo, Amedeo Gagliardi, Virginia Alberini, Tomas Buchler, Vaclav Liska, Gaetano Gallo, Veronika Vymetalkova, Ludmila Vodickova, Pavel Vodicka, Barbara Pardini, Giulio Ferrero
Published in: Mutagenesis, 2024, ISSN 0267-8357
Publisher: Oxford University Press
DOI: 10.1093/mutage/geae015

Human postprandial responses to food and potential for precision nutrition

Author(s): Sarah E. Berry, Ana M. Valdes, David A. Drew, Francesco Asnicar, Mohsen Mazidi, Jonathan Wolf, Joan Capdevila, George Hadjigeorgiou, Richard Davies, Haya Al Khatib, Christopher Bonnett, Sajaysurya Ganesh, Elco Bakker, Deborah Hart, Massimo Mangino, Jordi Merino, Inba Linenberg, Patrick Wyatt, Jose M. Ordovas, Christopher D. Gardner, Linda M. Delahanty, Andrew T. Chan, Nicola Segata, Paul W. Franks
Published in: Nature Medicine, 2020, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-020-0934-0

A quantitative tumor‐wide analysis of morphological heterogeneity of colorectal adenocarcinoma

Author(s): Mihnea P Dragomir, Vlad Popovici, Simon Schallenberg, Martina Čarnogurská, David Horst, Rudolf Nenutil, Fred Bosman, Eva Budinská
Published in: The Journal of Pathology: Clinical Research, Issue 11, 2025, ISSN 2056-4538
Publisher: Wiley
DOI: 10.1002/2056-4538.70034

Low-dose irradiation of the gut improves the efficacy of PD-L1 blockade in metastatic cancer patients

Author(s): Jianzhou Chen, Antonin Levy, Ai-Ling Tian, Xuehan Huang, Guoxin Cai, Marine Fidelle, Conrad Rauber, Pierre Ly, Eugénie Pizzato, Lisa Sitterle, Gianmarco Piccinno, Peng Liu, Sylvère Durand, Misha Mao, Liwei Zhao, Valerio Iebba, Hannah Felchle, Anne-Laure Mallard de La Varende, Julius Clemens Fischer, Simon Thomas, Tim F. Greten, Jennifer C. Jones, Cecilia Monge, Sandra Demaria, Silvia Formenti, L
Published in: Cancer Cell, Issue 43, 2025, Page(s) 361-379.e10, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2025.02.010

Mediterranean Diet to Prevent the Development of Colon Diseases: A Meta-Analysis of Gut Microbiota Studies

Author(s): Illescas O, Rodríguez-Sosa M, Gariboldi M.
Published in: Nutrients, 2021, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13072234

Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity.

Author(s): Thomas AM, Asnicar F, Kroemer G, Segata N.
Published in: Appl Environ Microbiol., 2021, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/aem.00471-21

Molecular portraits of colorectal cancer morphological regions

Author(s): Eva Budinská, Martina Hrivňáková, Tina Catela Ivkovic, Marie Madrzyk, Rudolf Nenutil, Beatrix Bencsiková, Dagmar Al Tukmachi, Michaela Ručková, Lenka Zdražilová Dubská, Ondřej Slabý, Josef Feit, Mihnea-Paul Dragomir, Petra Borilova Linhartova, Sabine Tejpar, Vlad Popovici
Published in: eLife, Issue 12, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.86655

Gut Microbiota–Related Biomarkers in Immuno-Oncology

Author(s): Carolina Alves Costa Silva, Marine Fidelle, Andrew A. Almonte, Lisa Derosa, Laurence Zitvogel
Published in: Annual Review of Pharmacology and Toxicology, Issue 65, 2025, Page(s) 333-354, ISSN 0362-1642
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-pharmtox-061124-102218

Cancer Induces a Stress Ileopathy Depending on β-Adrenergic Receptors and Promoting Dysbiosis that Contributes to Carcinogenesis

Author(s): Yonekura S, Terrisse S, Alves Costa Silva C, Lafarge A, Iebba V, Ferrere G, Goubet AG, Fahrner JE, Lahmar I, Ueda K, Mansouri G, Pizzato E, Ly P, Mazzenga M, Thelemaque C, Fidelle M, Jaulin F, Cartry J, Deloger M, Aglave M, Droin N, Opolon P, Puget A, Mann F, Neunlist M, Bessard A, Aymeric L, Matysiak-Budnik T, Bosq J, Hofman P, Duong CPM, Ugolini S, Quiniou V, Berrard S, Ryffel B, Kepp O, Kroemer
Published in: Cancer Discovery, Issue 12, 2022, Page(s) 1128-1151, ISSN 2159-8274
Publisher: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-21-0999

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer

Author(s): Gianmarco Piccinno, Kelsey N. Thompson, Paolo Manghi, Andrew R. Ghazi, Andrew Maltez Thomas, Aitor Blanco-Míguez, Francesco Asnicar, Katarina Mladenovic, Federica Pinto, Federica Armanini, Michal Punčochář, Elisa Piperni, Vitor Heidrich, Gloria Fackelmann, Giulio Ferrero, Sonia Tarallo, Long H. Nguyen, Yan Yan, Nazim A. Keles, Bilge G. Tuna, Veronika Vymetalkova, Mario Trompetto, Vaclav Liska,
Published in: Nature Medicine, Issue 31, 2025, Page(s) 2416-2429, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-025-03693-9

Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study

Author(s): Paula Istvan, Einar Birkeland, Ekaterina Avershina, Ane S. Kværner, Vahid Bemanian, Barbara Pardini, Sonia Tarallo, Willem M. de Vos, Torbjørn Rognes, Paula Berstad, Trine B. Rounge
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-46033-0

Oncobiomics: Leveraging Microbiome Translational Research in Immuno-Oncology for Clinical-Practice Changes

Author(s): Carolina Alves Costa Silva, Andrew A. Almonte, Laurence Zitvogel
Published in: Biomolecules, Issue 15, 2025, Page(s) 504, ISSN 2218-273X
Publisher: MDPI AG
DOI: 10.3390/biom15040504

TIGIT+ NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients

Author(s): Anastasia Tsakmaklis, Fedja Farowski, Rafael Zenner, Till Robin Lesker, Till Strowig, Hans Schlößer, Jonas Lehmann, Michael von Bergwelt-Baildon, Cornelia Mauch, Max Schlaak, Jana Knuever, Viola Schweinsberg, Lucie M. Heinzerling, Maria J. G. T. Vehreschild
Published in: BMC Cancer, Issue 23, 2023, ISSN 1471-2407
Publisher: BioMed Central
DOI: 10.1186/s12885-023-11551-5

Search for Mutations Connected With Non‐Response to Anti‐<scp>EGFR</scp> Therapy in <scp>mCRC</scp> in the Morphologically Defined Regions of Primary Tumours

Author(s): Martina Čarnogurská, Valeriia Serhiivna Vasylieva, Táňa Macháčková, Marie Boudná, Lucie Pifková, Jana Orlíčková, Tina Catela Ivkovic, Ondrej Slabý, Beatrix Bencsiková, Vlad Popovici, Eva Budinská
Published in: Cancer Medicine, Issue 14, 2025, ISSN 2045-7634
Publisher: Wiley
DOI: 10.1002/cam4.70910

Gut Microbiota in Immuno-Oncology: A Practical Guide for Medical Oncologists With a Focus on Antibiotics Stewardship

Author(s): Arielle Elkrief, Bertrand Routy, Lisa Derosa, Laura Bolte, Jennifer A. Wargo, Jennifer L. McQuade, Laurence Zitvogel
Published in: American Society of Clinical Oncology Educational Book, Issue 45, 2025, ISSN 1548-8748
Publisher: American Society of Clinical Oncology (ASCO)
DOI: 10.1200/edbk-25-472902

Formyl peptide receptor-1 (FPR1) represses intestinal oncogenesis

Author(s): Julie Le Naour, Léa Montégut, Yuhong Pan, Sarah Adriana Scuderi, Pierre Cordier, Adrien Joseph, Allan Sauvat, Valerio Iebba, Juliette Paillet, Gladys Ferrere, Ludivine Brechard, Claire Mulot, Grégory Dubourg, Laurence Zitvogel, Jonathan G. Pol, Erika Vacchelli, Pierre-Laurent Puig, Guido Kroemer
Published in: OncoImmunology, Issue 12, 2024, ISSN 2162-4011
Publisher: Landes Bioscience
DOI: 10.1080/2162402x.2023.2237354

Colorectal Tumour Mucosa Microbiome Is Enriched in Oral Pathogens and Defines Three Subtypes That Correlate with Markers of Tumour Progression.

Author(s): Barbora Zwinsová; Vyacheslav A. Petrov; Martina Hrivňáková; Stanislav Smatana; Stanislav Smatana; Lenka Micenková; Natálie Kazdová; Vlad Popovici; Roman Hrstka; Roman Šefr; Beatrix Bencsiková; Lenka Zdražilová-Dubská; Veronika Brychtová; Rudolf Nenutil; Petra Vídeňská; Eva Budinská
Published in: Volume 13, Issue 1, 2021, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13194799

Intellectual Property Rights

Patent (2)

A PREDICTIVE SCORE OF CANCER IMMUNOTHERAPY OUTCOME BASED ON ECOLOGICAL ANALYSIS OF GUT MICROBIOTA

Application/Publication number: 20 23080606
Date: 2023-11-02
Applicant(s): INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE

A PREDICTIVE SCORE OF CANCER IMMUNOTHERAPY OUTCOME BASED ON ECOLOGICAL ANALYSIS OF GUT MICROBIOTA

Application/Publication number: 20 23080606
Date: 2023-11-02
Applicant(s): INSTITUT GUSTAVE ROUSSY