Opendata, web and dolomites

PopMet

Investigating bacterial strain evolution through metagenomic genome assemblies

Total Cost €

0

EC-Contrib. €

0

Partnership

0

Views

0

Project "PopMet" data sheet

The following table provides information about the project.

Coordinator
EUROPEAN MOLECULAR BIOLOGY LABORATORY 

Organization address
address: Meyerhofstrasse 1
city: HEIDELBERG
postcode: 69117
website: http://www.embl.de

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 Germany [DE]
 Project website https://github.com/hildebra/Rarefaction
 Total cost 159˙460 €
 EC max contribution 159˙460 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2014
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2015
 Duration (year-month-day) from 2015-03-01   to  2017-02-28

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) coordinator 159˙460.00

Map

 Project objective

Recent advances in metagenomics have revealed considerable genetic variation among the microbes that populate the human gut. It has been shown that multiple strains of a bacterial species can coexist in a microbial community. However, accurately differentiating strains in metagenomic samples is mostly not possible, even though pathogenicity is usually strain specific. Therefore, I propose to utilize single nucleotide variants (SNVs) to (i) identify and delineate bacterial strains and to (ii) reconstruct single strain genomes. As more than 1,000 metagenomic samples are available, a large database of bacterial genomes from natural environments will be built and made publicly available. This will give the opportunity to investigate the role of adaptive evolution, mutation rate variation between hosts and the colonization history of bacterial strains among humans, all with high confidence due to the sheer data volume. Further, I plan to explore rare SNVs (nucleotide variants segregating at very low frequencies) that many population genetic methods are reliant on. This will be of particular significance, as it will provide insights into growth dynamics of bacterial communities in natural environments, benefiting both evolutionary and clinical research. Thus, the PopMet project is the application of POPulation genetic analysis on large METagenomic datasets.

 Publications

year authors and title journal last update
List of publications.
2017 Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wuellner U
Microbial, functional and viral gut metagenome shifts in early stage L-DOPA naive PD patients
published pages: , ISSN: 1756-994X, DOI:
Genome Medicine 2019-07-24
2016 Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R.
Gut Microbiota Linked to Sexual Preference and HIV Infection
published pages: 135-146, ISSN: 2352-3964, DOI: 10.1016/j.ebiom.2016.01.032
EBioMedicine Volume 5 2019-07-24
2016 S. S. Li, A. Zhu, V. Benes, P. I. Costea, R. Hercog, F. Hildebrand, J. Huerta-Cepas, M. Nieuwdorp, J. Salojarvi, A. Y. Voigt, G. Zeller, S. Sunagawa, W. M. de Vos, P. Bork
Durable coexistence of donor and recipient strains after fecal microbiota transplantation
published pages: 586-589, ISSN: 0036-8075, DOI: 10.1126/science.aad8852
Science 352/6285 2019-07-24
2016 Helle Krogh Pedersen, Valborg Gudmundsdottir, Henrik Bjørn Nielsen, Tuulia Hyotylainen, Trine Nielsen, Benjamin A. H. Jensen, Kristoffer Forslund, Falk Hildebrand, Edi Prifti, Gwen Falony, Emmanuelle Le Chatelier, Florence Levenez, Joel Doré, Ismo Mattila, Damian R. Plichta, Päivi Pöhö, Lars I. Hellgren, Manimozhiyan Arumugam, Shinichi Sunagawa, Sara Vieira-Silva, Torben Jørgensen, Jacob Bak Holm, Kajetan Trošt, MetaHIT Consortium, Karsten Kristiansen, Susanne Brix, Jeroen Raes, Jun Wang, Torben Hansen, Peer Bork, Søren Brunak, Matej Oresic, S. Dusko Ehrlich, Oluf Pedersen
Human gut microbes impact host serum metabolome and insulin sensitivity
published pages: 376-381, ISSN: 0028-0836, DOI: 10.1038/nature18646
Nature 535/7612 2019-07-24
2017 Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand
RTK: efficient rarefaction analysis of large datasets
published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btx206
Bioinformatics 2019-07-24
2015 Kristoffer Forslund, Falk Hildebrand, Trine Nielsen, Gwen Falony, Emmanuelle Le Chatelier, Shinichi Sunagawa, Edi Prifti, Sara Vieira-Silva, Valborg Gudmundsdottir, Helle Krogh Pedersen, Manimozhiyan Arumugam, Karsten Kristiansen, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul Igor Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, H. Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork, Oluf Pedersen
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
published pages: 262-266, ISSN: 0028-0836, DOI: 10.1038/nature15766
Nature 528/7581 2019-07-24

Are you the coordinator (or a participant) of this project? Plaese send me more information about the "POPMET" project.

For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an  email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.

Thanks. And then put a link of this page into your project's website.

The information about "POPMET" are provided by the European Opendata Portal: CORDIS opendata.

More projects from the same programme (H2020-EU.1.3.2.)

QuanToPol (2020)

Quantum Topological Polaritonics

Read More  

RegARcis (2020)

Role of the SWI/SNF complex in the Androgen Receptor cistrome regulation

Read More  

NaWaTL (2020)

Narrative, Writing, and the Teotihuacan Language: Exploring Language History Through Phylogenetics, Epigraphy and Iconography

Read More