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MicrobioS SIGNED

Exploring the human gut microbiome at strain resolution

Total Cost €

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EC-Contrib. €

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Partnership

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Project "MicrobioS" 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]
 Total cost 2˙184˙432 €
 EC max contribution 2˙184˙432 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2016
 Duration (year-month-day) from 2016-07-01   to  2021-06-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) coordinator 2˙184˙432.00

Map

 Project objective

With the genome sequencing of hundreds of bacterial isolates per day and a vast and growing number of metagenomic sequencing projects on gut microbiomes in healthy and diseased people all over the world, it becomes feasible to explore the microbial diversity in us not only at the level of genera and species, but at strains. As two different strains of a prokaryotic species might only share 40% of the genes and can also have vastly differ in single nucleotide polymorphism (SNP) many aspects of a proper understanding of the microbial communities we host in the gut might only be revealed at this high resolution level. This proposal aims (i) to develop a robust methodology to characterize the SNP and gene content landscape from metagenomic shotgun data (ii) to explore patterns of variation in the human population to stratify geographically, but also in subpopulations such as families and to understand spreading patterns and the evolution of microbial strains as well as iii) to work towards medical applications, for example by monitoring fecal microbiota transplantation (FMT) at strain resolution or monitoring particular strain of interest in the population

 Publications

year authors and title journal last update
List of publications.
2017 Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Subspecies in the global human gut microbiome
published pages: 960, ISSN: 1744-4292, DOI: 10.15252/msb.20177589
Molecular Systems Biology 13/12 2019-07-04
2017 J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients
published pages: , ISSN: 1756-994X, DOI: 10.1186/s13073-017-0428-y
Genome Medicine 9/1 2019-07-04
2017 Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
published pages: 2115-2122, ISSN: 0737-4038, DOI: 10.1093/molbev/msx148
Molecular Biology and Evolution 34/8 2019-07-04
2017 Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
metaSNV: A tool for metagenomic strain level analysis
published pages: e0182392, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0182392
PLOS ONE 12/7 2019-07-04
2017 J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients
published pages: , ISSN: 1756-994X, DOI: 10.1186/s13073-017-0451-z
Genome Medicine 9/1 2019-07-04
2016 Simone S. Li, Ana Zhu, Vladimir Benes, Paul I. Costea, Rajna Hercog, Falk Hildebrand, Jaime Huerta-Cepas, Max Nieuwdorp, Jarkko Salojärvi, Anita Y. Voigt, Georg Zeller, Shinichi Sunagawa, Willem M. de Vos, Peer 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 2019-05-22
2017 Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
published pages: D529-D534, ISSN: 0305-1048, DOI: 10.1093/nar/gkw989
Nucleic Acids Research 45/D1 2019-05-22
2019 Thomas SB Schmidt, Matthew R Hayward, Luis P Coelho, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato JC Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork
Extensive transmission of microbes along the gastrointestinal tract
published pages: , ISSN: 2050-084X, DOI: 10.7554/elife.42693
eLife 8 2019-04-18
2018 Thomas S.B. Schmidt, Jeroen Raes, Peer Bork
The Human Gut Microbiome: From Association to Modulation
published pages: 1198-1215, ISSN: 0092-8674, DOI: 10.1016/j.cell.2018.02.044
Cell 172/6 2019-04-18
2018 Katri Korpela, Paul Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I. Boomsma, Nicola Segata, Peer Bork
Selective maternal seeding and environment shape the human gut microbiome
published pages: 561-568, ISSN: 1088-9051, DOI: 10.1101/gr.233940.117
Genome Research 28/4 2019-04-18
2019 Falk Hildebrand, Lucas Moitinho-Silva, Sonja Blasche, Martin T Jahn, Toni Ingolf Gossmann, Jaime Huerta-Cepas, Rajna Hercog, Mechthild Luetge, Mohammad Bahram, Anna Pryszlak, Renato J Alves, Sebastian M Waszak, Ana Zhu, Lumeng Ye, Paul Igor Costea, Steven Aalvink, Clara Belzer, Sofia K Forslund, Shinichi Sunagawa, Ute Hentschel, Christoph Merten, Kiran Raosaheb Patil, Vladimir Benes, Peer Bork
Antibiotics-induced monodominance of a novel gut bacterial order
published pages: gutjnl-2018-3177, ISSN: 0017-5749, DOI: 10.1136/gutjnl-2018-317715
Gut 2019-04-18
2017 Julia Kleinteich, Falk Hildebrand, Mohammad Bahram, Anita Y. Voigt, Susanna A. Wood, Anne D. Jungblut, Frithjof C. Küpper, Antonio Quesada, Antonio Camacho, David A. Pearce, Peter Convey, Warwick F. Vincent, Christiane Zarfl, Peer Bork, Daniel R. Dietrich
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change
published pages: 1-11, ISSN: 2296-701X, DOI: 10.3389/fevo.2017.00137
Frontiers in Ecology and Evolution 5 2019-04-18
2018 Lisa Maier, Mihaela Pruteanu, Michael Kuhn, Georg Zeller, Anja Telzerow, Exene Erin Anderson, Ana Rita Brochado, Keith Conrad Fernandez, Hitomi Dose, Hirotada Mori, Kiran Raosaheb Patil, Peer Bork, Athanasios Typas
Extensive impact of non-antibiotic drugs on human gut bacteria
published pages: 623-628, ISSN: 0028-0836, DOI: 10.1038/nature25979
Nature 555/7698 2019-04-18
2018 Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
iPath3.0: interactive pathways explorer v3
published pages: W510-W513, ISSN: 0305-1048, DOI: 10.1093/nar/gky299
Nucleic Acids Research 46/W1 2019-04-18

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