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DiMeTrack

Assembly-based discovery of uncharacterized human microbiomemembers and their tracking across individuals and time

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

DiMeTrack project word cloud

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

prediction metagenomic discover temporal genome diagnostic association data plan individual diseases accurate metagenomes learning transmission policies taxonomically diseased causes unravelling few time underlying he shotgun publicly united fits functional databases monitor neonate track fulfil members supporting samples innovation microbial generation characterization dramatically machine mechanisms predictive newly genomes tool strain microbiome position mother uncharacterized compendium human wants healthy profile variability disease phenomena laboratory microbiology host biological microorganisms previously resolution roles first metagenomics people reintegrated tracking dark dimetrack profiling discovering 2020 detect expose assembly phylogenetically genetic tools horizon

Project "DiMeTrack" 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]
Project website	http://segatalab.cibio.unitn.it/
Total cost	180˙277 €
EC max contribution	180˙277 € (100%)
Programme	1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
Code Call	H2020-MSCA-IF-2015
Funding Scheme	MSCA-IF-EF-RI
Starting year	2016
Duration (year-month-day)	from 2016-10-01 to 2018-12-01

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	UNIVERSITA DEGLI STUDI DI TRENTO 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.	IT (TRENTO)	coordinator	180˙277.00

Map

Project objective

In this proposal we aim to expose and characterize members of the human-associated microbial dark matter and exploit the novel information to dramatically enhance the resolution of metagenomic profiling and develop accurate predictive/diagnostic tools. As a first step we will discover currently uncharacterized human microbiome members from metagenomic data through novel application of assembly-based approaches on a large compendium of newly generated and available shotgun metagenomes (Aim 1). The new identified genomes will be phylogenetically and taxonomically characterized and investigated to track strain-level individual and temporal genetic variability (Aim 2). The new genomes will be then used to develop a next generation host condition prediction approach through a genome-level machine learning tool (Aim 3). The three main objectives of the proposal are functional to the characterization of microbial dark matter from human microbiome and its use for strain-level microbiology tasks and metagenomic prediction/association tools. DiMeTrack focuses specifically on shotgun metagenomics and tracking across time and individual on many samples from publicly available databases and generated at the host laboratory. By discovering previously uncharacterized microorganisms and unravelling their roles in specific biological phenomena (e.g., mother-to-neonate transmission) and association with disease states, we fulfil the Horizon 2020 policies in supporting research and innovation that improve our understanding of the causes and mechanisms underlying healthy and diseased people and improve our ability to monitor and detect diseases. The profile and the future research plan of the applicant fits well with these research areas. In addition, after working in United States for a few years, he wants to be reintegrated in a research position in EU.

Publications

List of publications.
year	authors and title	journal	last update
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, Petra Schrotz-King, Cornelia M. Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller, Francesca Cordero, Emmanuel Dias-Neto, JoÃ£o Carlos Setubal, Adrian Tett, Barbara Pardini, Maria Rescigno, Levi Waldron, Alessio Naccarati, Nicola Segata 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	2019-06-11
2017	Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M CacciÃ², 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	2019-05-27
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	2019-05-22
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	2019-05-22
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	2019-05-22
2017	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: 2169-8287, DOI: 10.1128/genomea.01294-17	Genome Announcements 5/47	2019-05-22
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 Species Strains from a Freshwater Ecosystem published pages: , ISSN: 2169-8287, DOI: 10.1128/genomea.00009-18	Genome Announcements 6/5	2019-05-22
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 CrifÃ², Giuseppina Cusumano, Stefania Gottardi, Claudia Innamorati, Caterina MasÃ¨, 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	2019-05-22
2017	Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, Nicola Segata Microbial strain-level population structure and genetic diversity from metagenomes published pages: 626-638, ISSN: 1088-9051, DOI: 10.1101/gr.216242.116	Genome Research 27/4	2019-05-22
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	2019-05-22

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