Transmission of the human microbiome and its impact on health

Deliverables

Drafting of Data Management Plan

Publications

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

Author(s): Paolo Manghi, Aitor Blanco-Míguez, et al
Published in: Cell Reports, 2023, ISSN 2211-1247
Publisher: Amsterdam Elsevier
DOI: 10.1016/j.celrep.2023.112464

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts

Author(s): "Paolo Manghi # 1 2, Amrisha Bhosle # 3 4, Kai Wang # 3, Roberta Marconi # 1, Marta Selma-Royo 1, Liviana Ricci 1, Francesco Asnicar 1, Davide Golzato 1, Wenjie Ma 5, Dong Hang 3, Kelsey N Thompson 3 4, Eric A Franzosa 3 4, Amir Nabinejad 6, Sabrina Tambur"
Published in: nature microbiology, 2024, ISSN 2058-5276
Publisher: Nature portfolio
DOI: 10.1038/s41564-024-01858-9

The person-to-person transmission landscape of the gut and oral microbiomes

Author(s): Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D. Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moren
Published in: Nature, 2023, ISSN 1476-4687
Publisher: Springer Nature
DOI: 10.1038/s41586-022-05620-1

Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions

Author(s): Aitor Blanco-Míguez, Eric J.C. Gálvez, Edoardo Pasolli, Francesca De Filippis, Lena Amend, Kun D. Huang, Paolo Manghi, Till-Robin Lesker, Thomas Riedel, Linda Cova, Michal Punčochář, Andrew Maltez Thomas, Mireia Valles-Colomer, Isabel Schober, Thomas C.A. Hitch, Thomas Clavel, Sarah E. Berry, Richard Davies, Jonathan Wolf, Tim D. Spector, Jörg Overmann, Adrian Tett, Danilo Ercolini, Nicola Segata, Till Strowig
Published in: Cell Host & Microbe, Issue 31, 2024, ISSN 1931-3128
Publisher: Elsevier BV
DOI: 10.1016/j.chom.2023.09.013

Draft genome sequence of a representative strain of the Catenibacterium genus isolated from human feces

Author(s): Liviana Ricci, Marta Selma-Royo, Davide Golzato, Amir Nabinejad, Charlotte Servais, Federica Armanini, Francesco Asnicar, Federica Pinto, Sabrina Tamburini, Nicola Segata
Published in: Microbiology Resource Announcements, 2023, ISSN 2576-098X
Publisher: American Society for Microbiology
DOI: 10.1128/MRA.00329-23

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, 2023, ISSN 1759-4782
Publisher: Nature Portfolio
DOI: 10.1038/s41571-023-00785-8

Cell

Author(s): Niccolò Carlino1 ∙ Aitor Blanco-Míguez1 ∙ Michal Punčochář1 ∙ Claudia Mengoni1 ∙ Federica Pinto1 ∙ Alessia Tatti2,3,4 ∙ Paolo Manghi1 ∙ Federica Armanini1 ∙ Michele Avagliano5 ∙ Coral Barcenilla6 ∙ Samuel Breselge7,8 ∙ Raul Cabrera-Rubio7,9 ∙ Inés Calvete
Published in: Cell, Issue 187, 2024, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2024.07.039

Population-level impacts of antibiotic usage on the human gut microbiome

Author(s): Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41467-023-36633-7

Draft genome sequences of multiple bacterial strains isolated from human feces

Author(s): Marta Selma-Royo, Liviana Ricci, Davide Golzato, Charlotte Servais, Amir Nabinejad, Federica Armanini, Francesco Asnicar, Federica Pinto, Sabrina Tamburini, Nicola Segata
Published in: Microbiology Resource Announcements, Issue 13, 2024, ISSN 2576-098X
Publisher: American Society for Microbiology
DOI: 10.1128/mra.00307-24

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases

Author(s): Davide Bazzani, Vitor Heidrich, Paolo Manghi, Aitor Blanco-Miguez, Francesco Asnicar, Federica Armanini, Sara Cavaliere, Alberto Bertelle, Federico Dell’Acqua, Ester Dellasega, Romina Waldner, Daniela Vicentini, Mattia Bolzan, Cristiano Tomasi, Nicola Seg
Published in: npj Biofilms and Microbiomes, Issue 10, 2024, ISSN 2055-5008
Publisher: Springer Nature
DOI: 10.1038/s41522-024-00482-z

Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer

Author(s): Aitor Blanco-Míguez; Sara Carloni; Cindy Cardenas; Carola Conca Dioguardi; Luca Lambroia; Giovanni Capretti; Gennaro Nappo; Alessandro Fugazza; Antonio Capogreco; Federica Armanini; Francesco Asnicar; Leonard Dubois; Davide Golzato; Paolo Manghi; Federica Pinto; Cristina Scuderi; Erminia Casari; Marco Montorsi; Andrea Anderloni; Maria Rescigno; Alessandro Repici; Alessandro Zerbi; Clelia Peano; Sabrina Tamburini; Roberto Rusconi; Nicola Segata
Published in: npj Biofilms Microbiomes, 2024, ISSN 2055-5008
Publisher: nature portfolio
DOI: 10.1038/s41522-024-00506-8

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Author(s): Katherine M. Kennedy, Marcus C. de Goffau, Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D. Bushman, Joel Dore, Willem M. de Vos, Ashlee M. Earl, Jonathan A. Eisen, Michal A. Elovitz, Stephanie C. Ganal-Vonarburg, Michael G. Gänzle, Wendy S. Garrett, Lindsay J. Hall, Mathias W. Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J. Macpherson, Ruth C. Massey, Alice Carolyn McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O’Mahony, Paul W. O’Toole, Eric G. Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M. Sloboda, Gordon C. S. Smith, Harry Sokol, Tim D. Spector, Michael G. Surette, Gerald W. Tannock, Alan W. Walker, Moran Yassour, Jens Walter
Published in: Nature, Issue 613, 2023, ISSN 0028-0836
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41586-022-05546-8

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data

Author(s): Matteo Ciciani, Michele Demozzi, Eleonora Pedrazzoli, Elisabetta Visentin, Laura Pezzè, Lorenzo Federico Signorini, Aitor Blanco-Miguez, Moreno Zolfo, Francesco Asnicar, Antonio Casini, Anna Cereseto & Nicola Segata
Published in: Nature communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34213-9

Nature Communications

Author(s): Paolo Manghi, Michele Filosi, Moreno Zolfo, Lucas G. Casten, Albert Garcia-Valiente, Stefania Mattevi, Vitor Heidrich, Davide Golzato, Samuel Perini, Andrew M. Thomas, Simone Montalbano, Samuele Cancellieri, Levi Waldron, Jacob B. Hall, Simon Xu, Natalia
Published in: Nat Commun, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Portfolio
DOI: 10.1038/s41467-024-53934-7

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

Author(s): Blanco-Míguez, Aitor; Beghini, Francesco; Cumbo, Fabio; Mciver, Lauren J.; Thompson, Kelsey N.; Zolfo, Moreno; Manghi, Paolo; Dubois, Leonard; Huang, Kun D.; Thomas, Andrew Maltez; Nickols, William A.; Piccinno, Gianmarco; Piperni, Elisa; Punčochář, Micha
Published in: NATURE BIOTECHNOLOGY, Issue 41, 2023, ISSN 1087-0156
Publisher: Nature Portfolio
DOI: 10.1038/s41587-023-01688-w

Draft Genome Sequence of Neopoerus faecalis gen. nov., sp. nov., an Oscillospiraceae Strain Isolated from Human Feces

Author(s): Marta Selma-Royo https://orcid.org/0000-0002-4258-947X, Liviana Ricci https://orcid.org/0000-0001-9450-9235, Davide Golzato, Charlotte Servais, Federica Armanini, Francesco Asnicar, Federica Pinto, Nicola Segata
Published in: Microbiology Resource Announcements, 2023, ISSN 2576-098X
Publisher: American Society for Microbiology
DOI: 10.1128/mra.00330-23

Class-wide genomic tendency throughout specific extremes in black fungi

Author(s): Coleine, Claudia; Kurbessoian, Tania; Calia, Giulia; Delgado-Baquerizo, Manuel; Cestaro, Alessandro; Pindo, Massimo; Armanini, Federica; Asnicar, Francesco; Isola, Daniela; Segata, Nicola; Donati, Claudio; Stajich, Jason E.; de Hoog, Sybren; Selbmann, Laura
Published in: Fungal Diversity, vol 125, iss 1, 2024, ISSN 1878-9129
Publisher: springer
DOI: 10.1007/s13225-024-00533-y

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, Maristella Pitzalis, Jonathan Wolf, Jingyuan Fu, Alexandra Zhernakova, Simone M. Cacciò, Francesco Cucca, Sarah E. Berry, Danilo Ercolini, Andrew T. Chan, Curtis Huttenhower, Tim D. Spector, Nicola Segata, Francesco Asnicar
Published in: Cell, Issue 187, 2024, ISSN 0092-8674
Publisher: Elsevier BV
DOI: 10.1016/j.cell.2024.06.018

Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding

Author(s): Mireia Valles-Colomer, Paolo Manghi, Fabio Cumbo, Giulia Masetti, Federica Armanini, Francesco Asnicar, Aitor Blanco-Miguez, Federica Pinto, Michal Punčochář, Alberto Garaventa, Loredana Amoroso, Mirco Ponzoni, Maria Valeria Corrias, Nicola Segata
Published in: eBioMedicine, Issue 99, 2024, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2023.104917

Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective

Author(s): Mireia Valles-Colomer, Cristina Menni, Sarah E. Berry, Ana M. Valdes, Tim D. Spector, Nicola Segata
Published in: Nature Medicine, Issue 29, 2023, ISSN 1078-8956
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41591-023-02260-4

Machine learning for microbiologists

Author(s): Francesco Asnicar; Andrew Maltez Thomas; Andrea Passerini; Levi Waldron; Nicola Segata
Published in: Nat Rev Microbiol, 2023, ISSN 1740-1534
Publisher: nature portfolio
DOI: 10.1038/s41579-023-00984-1

CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing

Author(s): Eleonora Pedrazzoli, Michele Demozzi, Elisabetta Visentin, Matteo Ciciani, Ilaria Bonuzzi, Laura Pezzè, Lorenzo Lucchetta, Giulia Maule, Simone Amistadi, Federica Esposito, Mariangela Lupo, Annarita Miccio, Alberto Auricchio, Antonio Casini, Nicola Segata, Anna Cereseto
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41467-024-47800-9

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