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Exploring the human gut microbiome at strain resolution

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Publications

Subspecies in the global human gut microbiome

Author(s): Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Published in: Molecular Systems Biology, Issue 13/12, 2017, Page(s) 960, ISSN 1744-4292
DOI: 10.15252/msb.20177589

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

Author(s): J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Published in: Genome Medicine, Issue 9/1, 2017, ISSN 1756-994X
DOI: 10.1186/s13073-017-0428-y

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

Author(s): J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Published in: Genome Medicine, Issue 9/1, 2017, ISSN 1756-994X
DOI: 10.1186/s13073-017-0451-z

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Author(s): Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Published in: Molecular Biology and Evolution, Issue 34/8, 2017, Page(s) 2115-2122, ISSN 0737-4038
DOI: 10.1093/molbev/msx148

metaSNV: A tool for metagenomic strain level analysis

Author(s): Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Published in: PLOS ONE, Issue 12/7, 2017, Page(s) e0182392, ISSN 1932-6203
DOI: 10.1371/journal.pone.0182392

Extensive transmission of microbes along the gastrointestinal tract

Author(s): 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
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
DOI: 10.7554/elife.42693

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Author(s): 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
Published in: Frontiers in Ecology and Evolution, Issue 5, 2017, Page(s) 1-11, ISSN 2296-701X
DOI: 10.3389/fevo.2017.00137

Selective maternal seeding and environment shape the human gut microbiome

Author(s): Katri Korpela, Paul Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I. Boomsma, Nicola Segata, Peer Bork
Published in: Genome Research, Issue 28/4, 2018, Page(s) 561-568, ISSN 1088-9051
DOI: 10.1101/gr.233940.117

Antibiotics-induced monodominance of a novel gut bacterial order

Author(s): 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
Published in: Gut, 2019, Page(s) gutjnl-2018-317715, ISSN 0017-5749
DOI: 10.1136/gutjnl-2018-317715

Extensive impact of non-antibiotic drugs on human gut bacteria

Author(s): 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
Published in: Nature, Issue 555/7698, 2018, Page(s) 623-628, ISSN 0028-0836
DOI: 10.1038/nature25979

The Human Gut Microbiome: From Association to Modulation

Author(s): Thomas S.B. Schmidt, Jeroen Raes, Peer Bork
Published in: Cell, Issue 172/6, 2018, Page(s) 1198-1215, ISSN 0092-8674
DOI: 10.1016/j.cell.2018.02.044

iPath3.0: interactive pathways explorer v3

Author(s): Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W510-W513, ISSN 0305-1048
DOI: 10.1093/nar/gky299

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Author(s): Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D529-D534, ISSN 0305-1048
DOI: 10.1093/nar/gkw989

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

Author(s): 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
Published in: Science, Issue 352/6285, 2016, Page(s) 586-589, ISSN 0036-8075
DOI: 10.1126/science.aad8852