MetaPG SIGNED
Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world
Total Cost €
0EC-Contrib. €
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Project "MetaPG" data sheet
The following table provides information about the project.
| Coordinator |
UNIVERSITA DEGLI STUDI DI TRENTO
Organization address contact info |
| Coordinator Country | Italy [IT] |
| Total cost | 1˙499˙482 € |
| EC max contribution | 1˙499˙482 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2016-STG |
| Funding Scheme | ERC-STG |
| Starting year | 2017 |
| Duration (year-month-day) | from 2017-04-01 to 2022-03-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | UNIVERSITA DEGLI STUDI DI TRENTO | IT (TRENTO) | coordinator | 1˙499˙482.00 |
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Project objective
Investigating symbiotic gut microbes with large-scale comparative genomics would allow gaining crucial insights into the “epidemiology”, genetic diversity, and population structure of hundreds of scarcely characterized microorganisms. However, cultivation-based approaches are ineffective at targeting the large fraction of the gut microbial diversity that is hard be grown in vitro. They are also expensive and time consuming, as they need sampling specific bacteria from geographically separated subjects. On the other hand, cultivation-free metagenomic data is now available for thousands of stool samples collected worldwide, but they are not currently exploited for strain-level microbial population genomics because of the lack of suitable computational methods. In Aim1, we leverage our expertise in computational biology to bridge the gap between the fields of metagenomics and population genomics by developing novel and highly innovative methodologies to extract strain-level genomic and genetic profiles from metagenomic samples with the resolution needed by comparative genomics. Such paradigmatic shift will put us in the position of reusing in Aim2 the thousands of available metagenomes and unravel for the first time the population structure of hundreds of uncultivable gut microbes. Among the novel tasks enabled, we will focus in Aim3 on identifying those microbial strains that are currently disappearing in westernized populations as a consequence of urbanization, industrialization, high-fat diets. We will complement the available data with gut metagenomes from novel targeted cohorts of both westernized and non-westernized populations. Our project defines the foundation for cultivation-free strain-level population genomics, provides comparative genomics results with unprecedented resolution for hundreds of under-investigated microbes, and compiles a catalogue of strains undergoing or at risk of primary, secondary, or ecological extinction in westernized populations.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2018 |
Moran Yassour, Eeva Jason, Larson J. Hogstrom, Timothy D. Arthur, Surya Tripathi, Heli Siljander, Jenni Selvenius, Sami Oikarinen, Heikki Hyöty, Suvi M. Virtanen, Jorma Ilonen, Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Nicola Segata, Hera Vlamakis, Eric S. Lander, Curtis Huttenhower, Mikael Knip, Ramnik J. Xavier Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life published pages: 146-154.e4, ISSN: 1931-3128, DOI: 10.1016/j.chom.2018.06.007 |
Cell Host & Microbe 24/1 | 2019-12-16 |
| 2019 |
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 The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations published pages: 666-679.e7, ISSN: 1931-3128, DOI: 10.1016/j.chom.2019.08.018 |
Cell Host & Microbe 26/5 | 2019-11-22 |
| 2018 |
Serena Manara, Edoardo Pasolli, Daniela Dolce, Novella Ravenni, Silvia Campana, Federica Armanini, Francesco Asnicar, Alessio Mengoni, Luisa Galli, Carlotta Montagnani, Elisabetta Venturini, Omar Rota-Stabelli, Guido Grandi, Giovanni Taccetti, Nicola Segata Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital published pages: , ISSN: 1756-994X, DOI: 10.1186/s13073-018-0593-7 |
Genome Medicine 10/1 | 2019-11-22 |
| 2019 |
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 Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle published pages: 649-662.e20, ISSN: 0092-8674, DOI: 10.1016/j.cell.2019.01.001 |
Cell 176/3 | 2019-11-22 |
| 2019 |
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, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Jakob Wirbel, Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation published pages: 667-678, ISSN: 1078-8956, DOI: 10.1038/s41591-019-0405-7 |
Nature Medicine 25/4 | 2019-11-22 |
| 2018 |
Nicola Segata On the Road to Strain-Resolved Comparative Metagenomics published pages: , ISSN: 2379-5077, DOI: 10.1128/mSystems.00190-17 |
mSystems 3/2 | 2019-05-15 |
| 2018 |
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 Xavier, Carmen Maria Collado, Omry Koren, Saverio Tateo, Massimo Soffiati, Anna Pedrotti, Marco Ventura, Curtis Huttenhower, Peer Bork, Nicola Segata Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome published pages: 133-145.e5, ISSN: 1931-3128, DOI: 10.1016/j.chom.2018.06.005 |
Cell Host & Microbe 24/1 | 2019-05-15 |
| 2018 |
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata Profiling microbial strains in urban environments using metagenomic sequencing data published pages: , ISSN: 1745-6150, DOI: 10.1186/s13062-018-0211-z |
Biology Direct 13/1 | 2019-05-15 |
| 2017 |
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata Shotgun metagenomics, from sampling to analysis published pages: 833-844, ISSN: 1087-0156, DOI: 10.1038/nbt.3935 |
Nature Biotechnology 35/9 | 2019-05-15 |
| 2018 |
Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Adriano Boscaini, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater published pages: , ISSN: 2576-098X, DOI: |
Genome Announcements | 2019-05-15 |
| 2018 |
Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Adriano Boscaini, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata Draft genome sequences of novel Pseudomonas, Flavobacterium, and Sediminibacterium strains from a freshwater ecosystem published pages: , ISSN: 2576-098X, DOI: |
Microbiology Resource Announcements | 2019-05-15 |
| 2017 |
Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron Accessible, curated metagenomic data through ExperimentHub published pages: 1023-1024, ISSN: 1548-7091, DOI: 10.1038/nmeth.4468 |
Nature Methods 14/11 | 2019-05-15 |
| 2017 |
Adrian Tett, Edoardo Pasolli, Stefania Farina, Duy Tin Truong, Francesco Asnicar, Moreno Zolfo, Francesco Beghini, Federica Armanini, Olivier Jousson, Veronica De Sanctis, Roberto Bertorelli, Giampiero Girolomoni, Mario Cristofolini, Nicola Segata Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis published pages: , ISSN: 2055-5008, DOI: 10.1038/s41522-017-0022-5 |
npj Biofilms and Microbiomes 3/1 | 2019-05-15 |
| 2017 |
Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M Cacciò, Nicola Segata Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome published pages: 2848-2863, ISSN: 1751-7362, DOI: 10.1038/ismej.2017.139 |
The ISME Journal 11/12 | 2019-05-15 |
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