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Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world

Total Cost €


EC-Contrib. €






 MetaPG project word cloud

Explore the words cloud of the MetaPG project. It provides you a very rough idea of what is the project "MetaPG" about.

epidemiology    genetic    population    sampling    industrialization    strains    first    urbanization    biology    genomic    put    data    populations    grown    diets    consuming    catalogue    undergoing    metagenomes    gut    microorganisms    strain    secondary    microbial    metagenomics    samples    thousands    uncultivable    gap    lack    hundreds    unprecedented    gaining    suitable    provides    resolution    consequence    symbiotic    position    fat    computational    primary    scarcely    diversity    risk    enabled    reusing    fraction    profiles    geographically    innovative    extinction    aim2    investigating    structure    hard    genomics    disappearing    complement    westernized    defines    foundation    paradigmatic    collected    exploited    stool    unravel    expertise    leverage    expensive    subjects    worldwide    extract    microbes    compiles    separated    insights    aim1    shift    time    free    ecological    bridge    vitro    ineffective    cultivation    aim3    bacteria    cohorts    metagenomic   

Project "MetaPG" data sheet

The following table provides information about the project.


Organization address
address: VIA CALEPINA 14
city: TRENTO
postcode: 38122

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 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


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITA DEGLI STUDI DI TRENTO IT (TRENTO) coordinator 1˙499˙482.00


 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.


year authors and title journal last update
List of publications.
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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