F
Francesco Beghini
Researcher at University of Trento
Publications - 28
Citations - 4529
Francesco Beghini is an academic researcher from University of Trento. The author has contributed to research in topics: Microbiome & Metagenomics. The author has an hindex of 12, co-authored 24 publications receiving 1906 citations. Previous affiliations of Francesco Beghini include University of British Columbia.
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Journal ArticleDOI
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Edoardo Pasolli,Francesco Asnicar,Serena Manara,Moreno Zolfo,Nicolai Karcher,Federica Armanini,Francesco Beghini,Paolo Manghi,Adrian Tett,Paolo Ghensi,Maria Carmen Collado,Benjamin L. Rice,Casey DuLong,Xochitl C. Morgan,Christopher D. Golden,Christopher Quince,Curtis Huttenhower,Nicola Segata +17 more
TL;DR: Thousands of microbial genomes from yet-to-be-named species are identified, the pangenomes of human-associated microbes are expanded, and better exploitation of metagenomic technologies are allowed.
Journal ArticleDOI
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.
Pamela Ferretti,Edoardo Pasolli,Adrian Tett,Francesco Asnicar,Valentina Gorfer,Sabina Fedi,Federica Armanini,Duy Tin Truong,Serena Manara,Moreno Zolfo,Francesco Beghini,Roberto Bertorelli,Veronica De Sanctis,Ilaria Bariletti,Rosarita Canto,Rosanna Clementi,Marina Cologna,Tiziana Crifò,Giuseppina Cusumano,Stefania Gottardi,Claudia Innamorati,Caterina Masè,Daniela Postai,Daniela Savoi,Sabrina Duranti,Gabriele Andrea Lugli,Leonardo Mancabelli,Francesca Turroni,Chiara Ferrario,Christian Milani,Marta Mangifesta,Rosaria Anzalone,Alice Viappiani,Moran Yassour,Hera Vlamakis,Ramnik J. Xavier,Carmen Maria Collado,Omry Koren,Saverio Tateo,Massimo Soffiati,Anna Pedrotti,Marco Ventura,Curtis Huttenhower,Curtis Huttenhower,Peer Bork,Nicola Segata +45 more
TL;DR: The mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome are described, including maternal gut strains that proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources.
Journal ArticleDOI
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3
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,Nicola Segata +23 more
TL;DR: BioBakery 3 as mentioned in this paper is a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available.
Journal ArticleDOI
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
Andrew Maltez Thomas,Andrew Maltez Thomas,Paolo Manghi,Francesco Asnicar,Edoardo Pasolli,Federica Armanini,Moreno Zolfo,Francesco Beghini,Serena Manara,Nicolai Karcher,Chiara Pozzi,Sara Gandini,Davide Serrano,Sonia Tarallo,Antonio Francavilla,Gaetano Gallo,Mario Trompetto,Giulio Ferrero,Sayaka Mizutani,Sayaka Mizutani,Hirotsugu Shiroma,Satoshi Shiba,Tatsuhiro Shibata,Shinichi Yachida,Takuji Yamada,Takuji Yamada,Jakob Wirbel,Petra Schrotz-King,Cornelia M. Ulrich,Hermann Brenner,Manimozhiyan Arumugam,Manimozhiyan Arumugam,Peer Bork,Georg Zeller,Francesca Cordero,Emmanuel Dias-Neto,João C. Setubal,João C. Setubal,Adrian Tett,Barbara Pardini,Maria Rescigno,Levi Waldron,Alessio Naccarati,Nicola Segata +43 more
TL;DR: The combined analysis of heterogeneous CRC cohorts identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.
Posted ContentDOI
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini,Lauren J. McIver,Aitor Blanco-Míguez,Leonard Dubois,Francesco Asnicar,Sagun Maharjan,Sagun Maharjan,Ana Mailyan,Ana Mailyan,Andrew Maltez Thomas,Paolo Manghi,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,Nicola Segata +22 more
TL;DR: With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.