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MicrobioS SIGNED

Exploring the human gut microbiome at strain resolution

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

MicrobioS project word cloud

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

stratify vast understand data spreading monitoring genes day fmt microbiota shotgun human people with sequencing microbial methodology families prokaryotic medical isolates microbiomes fecal vastly population host 40 diseased strain gut genera snp species variation content genome landscape gene explore becomes diversity feasible hundreds polymorphism differ revealed world communities bacterial patterns subpopulations geographically transplantation share proper single evolution metagenomic strains resolution nucleotide healthy

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 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.	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

List of publications.
year	authors and title	journal	last update
2017	Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huertaâ€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. WÃ¼llner Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naÃ¯ve Parkinsonâ€™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. WÃ¼llner Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naÃ¯ve Parkinsonâ€™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 SalojÃ¤rvi, 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. KÃ¼pper, 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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