Exploring the human gut microbiome at strain resolution

Publications

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology

Author(s): Falk Hildebrand, Mark J Pallen, Peer Bork
Published in: Gut, Issue 69/7, 2020, Page(s) 1358.1-1359, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2019-319045

Diversity within species: interpreting strains in microbiomes

Author(s): Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork
Published in: Nature Reviews Microbiology, Issue 18/9, 2020, Page(s) 491-506, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-020-0368-1

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

Author(s): Anne-Claude Gavin; Peer Bork; Yuanyue Li; Michael Kuhn
Published in: Bioinformatics (2019), Issue 1, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/573790

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Author(s): Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, Thomas S B Schmidt, Alessio Milanese, Lucas Paoli, Ana Hernández-Plaza, Askarbek N Orakov, Sofia K Forslund, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Luis Pedro Coelho, Peer Bork
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1002

Combinatorial, additive and dose-dependent drug–microbiome associations

Author(s): "Forslund, S.*, Chakaroun, R.*, Zimmermann-Kogodeeva, M.* …[36 authors].... Metacardis consortium ....[14 authors]… Clement, K#, Stumvogel, M.# and Bork, P.#"
Published in: Nature, 2021, ISSN 1476-4687
Publisher: Springer Nature
DOI: 10.1038/s41586-021-04177-9

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Author(s): Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S. Fleck, Anita Y. Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Niméus, Andrew M. Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinich
Published in: Nature Medicine, Issue 25/4, 2019, Page(s) 679-689, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-019-0406-6

A fecal microbiota signature with high specificity for pancreatic cancer

Author(s): "Kartal, E.*, Schmidt, S.*, Molina-Montes, E.* ...[21 authors]... PanGenEU study investigators, Benes, V., Zeller, G., Real, F.X., Malats, N.# And Bork, P.#"
Published in: Gut, 2022, ISSN 1468-3288
Publisher: BMJ publishing group
DOI: 10.1136/gutjnl-2021-324755

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Author(s): Ivica Letunic, Peer Bork
Published in: Nucleic Acids Research, Issue 47/W1, 2019, Page(s) W256-W259, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz239

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Author(s): Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P. and Huerta-Cepas, J.
Published in: Molecular Biology and Evolution, 2021, ISSN 1537-1719
Publisher: Oxford Academic
DOI: 10.1093/molbev/msab293

GUNC: detection of chimerism and contamination in prokaryotic genomes

Author(s): Orakov, A.N., Fullam, A.N., Coelho, L.P., Khefkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P.
Published in: Genome Biology, 2021, ISSN 1474-760X
Publisher: Biomed central - springer nature
DOI: 10.1186/s13059-021-02393-0

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Author(s): Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Published in: Microbiome, Issue 7/1, 2019, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-019-0684-8

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
Publisher: Nature Publishing Group
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
Publisher: BioMed Central
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

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
Publisher: Oxford University Press
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
Publisher: Public Library of Science
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
Publisher: eLife Sciences Publications
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
Publisher: Frontiers
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
Publisher: Cold Spring Harbor Laboratory Press
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
Publisher: BMJ Publishing Group
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
Publisher: Nature Publishing Group
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
Publisher: Cell Press
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
Publisher: Oxford University Press
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
Publisher: Oxford University Press
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
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aad8852

Dispersal strategies shape persistence and evolution of gut bacteria

Author(s): Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Bahram, M., Nielsen, H.B. and Bork, P.
Published in: Cell Host & Microbe, 2021, ISSN 1934-6069
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.05.008

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Author(s): Huerta-Cepas, J.*, Szklarczyk, D.*, Heller, D., Hernandez-Plaza, A., Forslund, S.K., Cook, H., Mende, D., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C. and Bork, P.
Published in: NAR, 2019, ISSN 1362-4962
Publisher: Oxford Academics
DOI: 10.1093/nar/gky1085

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Author(s): Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Published in: The ISME Journal, Issue 14/5, 2020, Page(s) 1247-1259, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-020-0600-z

SMART: recent updates, new developments and status in 2020

Author(s): Ivica Letunic, Supriya Khedkar, Peer Bork
Published in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D458-D460, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa937

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

Author(s): Van Rossum, T., Costea, P., Paoli, L., Alves, R., Thielemann, R., Sunugava, S. and Bork., P.
Published in: Bioinformatics, 2022, ISSN 1460-2059
Publisher: oxford university press
DOI: 10.1093/bioinformatics/btab789

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment

Author(s): Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
Published in: Environmental Microbiology Reports, Issue 11/4, 2019, Page(s) 487-494, ISSN 1758-2229
Publisher: Wiley-Blackwell
DOI: 10.1111/1758-2229.12684

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Author(s): Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, Edoardo Pasolli, Federica Armanini, Moreno Zolfo, Francesco Beghini, Serena Manara, Nicolai Karcher, Chiara Pozzi, Sara Gandini, Davide Serrano, Sonia Tarallo, Antonio Francavilla, Gaetano Gallo, Mario Trompetto, Giulio Ferrero, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Jakob Wirbel,
Published in: Nature Medicine, Issue 25/4, 2019, Page(s) 667-678, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-019-0405-7

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