PopMet
Investigating bacterial strain evolution through metagenomic genome assemblies
Total Cost €
0EC-Contrib. €
0Partnership
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Project "PopMet" data sheet
The following table provides information about the project.
| Coordinator |
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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, RodrÃguez 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 |
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