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MetaPG SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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

Project "MetaPG" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITA DEGLI STUDI DI TRENTO 

Organization address
address: VIA CALEPINA 14
city: TRENTO
postcode: 38122
website: www.unitn.it

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

 Partnership

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

Map

 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
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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