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

Livrables

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

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

ONCOBIOME logo and graphic chart

Publications

Gut microbiota composition in colorectal cancer patients is genetically regulated

Auteurs: 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
Publié dans: Scientific Reports, Numéro 12, 2022, Page(s) 11424, ISSN 2045-2322
Éditeur: 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

Auteurs: 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
Publié dans: Nature Medicine, 2022, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-022-01964-3

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

Auteurs: Pačínková A., Popovici V.
Publié dans: BMC Bioinformatics, Numéro 23, 2022, Page(s) 351, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-022-04891-9

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

Auteurs: 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
Publié dans: Nature Medicine, Numéro 28, 2022, Page(s) 315-324, ISSN 1078-8956
Éditeur: 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.

Auteurs: 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
Publié dans: Gut, Numéro 7, 2021, ISSN 0017-5749
Éditeur: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-323877

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

Auteurs: Ferrero G, Carpi S, Polini B, Pardini B, Nieri P, Impeduglia A, Grioni S, Tarallo S, Naccarati A.
Publié dans: Frontiers in pharmacology., 2021, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2020.619200

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

Auteurs: 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
Publié dans: eLife, Numéro 2, 2021, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.65088

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

Auteurs: 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
Publié dans: Nature Medicine, 2021, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-020-01183-8

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

Auteurs: 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
Publié dans: Cancer Medicine, Numéro 00, 2022, Page(s) 1-15, ISSN 2045-7634
Éditeur: John Wiley & Sons Ltd
DOI: 10.1002/cam4.5375

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

Auteurs: 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
Publié dans: Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021), Numéro 2, 2021, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-00014-1

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

Auteurs: 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.
Publié dans: Genome Biology, Numéro 9, 2020, ISSN 1474-7596
Éditeur: BioMed Central
DOI: 10.1186/s13059-020-02042-y

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

Auteurs: 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
Publié dans: Gut, Numéro 1, 2021, ISSN 1468-3288
Éditeur: BMJ
DOI: 10.1136/gutjnl-2021-325168

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

Auteurs: Sander Wuyts, Nicola Segata
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: Springer Nature
DOI: 10.1186/s13059-019-1714-3

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

Auteurs: 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
Publié dans: Cell Host & Microbe, Numéro 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
Éditeur: Cell Press
DOI: 10.1016/j.chom.2019.08.018

Multiple levels of the unknown in microbiome research

Auteurs: Andrew Maltez Thomas, Nicola Segata
Publié dans: BMC Biology, Numéro 17/1, 2019, ISSN 1741-7007
Éditeur: BioMed Central
DOI: 10.1186/s12915-019-0667-z

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

Auteurs: 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
Publié dans: mSystems, Numéro 4/5, 2019, ISSN 2379-5077
Éditeur: American Society for Microbiology Journals
DOI: 10.1128/mSystems.00289-19

Detecting contamination in viromes using ViromeQC

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

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Genome Biology, Numéro 4, 2021, ISSN 1474-7596
Éditeur: BioMed Central
DOI: 10.1186/s13059-021-02427-7

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

Auteurs: 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
Publié dans: Nature Biotechnology, 2023, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-023-01688-w

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

Auteurs: 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
Publié dans: Nature Medicine, Numéro 28, 2022, Page(s) 535-544, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-022-01695-5

Prevotella diversity, niches and interactions with the human host

Auteurs: Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini, Nicola Segata
Publié dans: Nature reviews. Microbiology, 2021, ISSN 1740-1526
Éditeur: Nature Publishing Group
DOI: 10.1038/s41579-021-00559-y

Human postprandial responses to food and potential for precision nutrition

Auteurs: 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
Publié dans: Nature Medicine, 2020, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-020-0934-0

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

Auteurs: Illescas O, Rodríguez-Sosa M, Gariboldi M.
Publié dans: Nutrients, 2021, ISSN 2072-6643
Éditeur: 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.

Auteurs: Thomas AM, Asnicar F, Kroemer G, Segata N.
Publié dans: Appl Environ Microbiol., 2021, ISSN 0099-2240
Éditeur: American Society for Microbiology
DOI: 10.1128/aem.00471-21

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

Auteurs: 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
Publié dans: Cancer Discovery, Numéro 12, 2022, Page(s) 1128-1151, ISSN 2159-8274
Éditeur: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-21-0999

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

Auteurs: 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
Publié dans: Volume 13, Numéro 1, 2021, ISSN 2072-6694
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13194799

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