Exploring the human gut microbiome at strain resolution

Pubblicazioni

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

Autori: Falk Hildebrand, Mark J Pallen, Peer Bork
Pubblicato in: Gut, Numero 69/7, 2020, Pagina/e 1358.1-1359, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2019-319045

Diversity within species: interpreting strains in microbiomes

Autori: Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork
Pubblicato in: Nature Reviews Microbiology, Numero 18/9, 2020, Pagina/e 491-506, ISSN 1740-1526
Editore: 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

Autori: Anne-Claude Gavin; Peer Bork; Yuanyue Li; Michael Kuhn
Pubblicato in: Bioinformatics (2019), Numero 1, 2019, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1101/573790

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

Autori: 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
Pubblicato in: Nucleic Acids Research, 2019, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz1002

Combinatorial, additive and dose-dependent drug–microbiome associations

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

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

Autori: 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
Pubblicato in: Nature Medicine, Numero 25/4, 2019, Pagina/e 679-689, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-019-0406-6

A fecal microbiota signature with high specificity for pancreatic cancer

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

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

Autori: Ivica Letunic, Peer Bork
Pubblicato in: Nucleic Acids Research, Numero 47/W1, 2019, Pagina/e W256-W259, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz239

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

Autori: Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P. and Huerta-Cepas, J.
Pubblicato in: Molecular Biology and Evolution, 2021, ISSN 1537-1719
Editore: Oxford Academic
DOI: 10.1093/molbev/msab293

GUNC: detection of chimerism and contamination in prokaryotic genomes

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

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

Autori: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Pubblicato in: Microbiome, Numero 7/1, 2019, ISSN 2049-2618
Editore: Springer Nature
DOI: 10.1186/s40168-019-0684-8

Subspecies in the global human gut microbiome

Autori: Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Pubblicato in: Molecular Systems Biology, Numero 13/12, 2017, Pagina/e 960, ISSN 1744-4292
Editore: 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

Autori: J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork, U. Wüllner
Pubblicato in: Genome Medicine, Numero 9/1, 2017, ISSN 1756-994X
Editore: 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

Autori: Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Pubblicato in: Molecular Biology and Evolution, Numero 34/8, 2017, Pagina/e 2115-2122, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msx148

metaSNV: A tool for metagenomic strain level analysis

Autori: Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Pubblicato in: PLOS ONE, Numero 12/7, 2017, Pagina/e e0182392, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0182392

Extensive transmission of microbes along the gastrointestinal tract

Autori: 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
Pubblicato in: eLife, Numero 8, 2019, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.42693

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

Autori: 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
Pubblicato in: Frontiers in Ecology and Evolution, Numero 5, 2017, Pagina/e 1-11, ISSN 2296-701X
Editore: Frontiers
DOI: 10.3389/fevo.2017.00137

Selective maternal seeding and environment shape the human gut microbiome

Autori: Katri Korpela, Paul Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I. Boomsma, Nicola Segata, Peer Bork
Pubblicato in: Genome Research, Numero 28/4, 2018, Pagina/e 561-568, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.233940.117

Antibiotics-induced monodominance of a novel gut bacterial order

Autori: 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
Pubblicato in: Gut, 2019, Pagina/e gutjnl-2018-317715, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2018-317715

Extensive impact of non-antibiotic drugs on human gut bacteria

Autori: 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
Pubblicato in: Nature, Numero 555/7698, 2018, Pagina/e 623-628, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/nature25979

The Human Gut Microbiome: From Association to Modulation

Autori: Thomas S.B. Schmidt, Jeroen Raes, Peer Bork
Pubblicato in: Cell, Numero 172/6, 2018, Pagina/e 1198-1215, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2018.02.044

iPath3.0: interactive pathways explorer v3

Autori: Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
Pubblicato in: Nucleic Acids Research, Numero 46/W1, 2018, Pagina/e W510-W513, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gky299

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

Autori: Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Pubblicato in: Nucleic Acids Research, Numero 45/D1, 2017, Pagina/e D529-D534, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw989

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

Autori: 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
Pubblicato in: Science, Numero 352/6285, 2016, Pagina/e 586-589, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.aad8852

Dispersal strategies shape persistence and evolution of gut bacteria

Autori: Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Bahram, M., Nielsen, H.B. and Bork, P.
Pubblicato in: Cell Host & Microbe, 2021, ISSN 1934-6069
Editore: 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

Autori: 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.
Pubblicato in: NAR, 2019, ISSN 1362-4962
Editore: Oxford Academics
DOI: 10.1093/nar/gky1085

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

Autori: 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
Pubblicato in: The ISME Journal, Numero 14/5, 2020, Pagina/e 1247-1259, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/s41396-020-0600-z

SMART: recent updates, new developments and status in 2020

Autori: Ivica Letunic, Supriya Khedkar, Peer Bork
Pubblicato in: Nucleic Acids Research, Numero 49/D1, 2020, Pagina/e D458-D460, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa937

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

Autori: Van Rossum, T., Costea, P., Paoli, L., Alves, R., Thielemann, R., Sunugava, S. and Bork., P.
Pubblicato in: Bioinformatics, 2022, ISSN 1460-2059
Editore: oxford university press
DOI: 10.1093/bioinformatics/btab789

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

Autori: Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
Pubblicato in: Environmental Microbiology Reports, Numero 11/4, 2019, Pagina/e 487-494, ISSN 1758-2229
Editore: 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

Autori: 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,
Pubblicato in: Nature Medicine, Numero 25/4, 2019, Pagina/e 667-678, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-019-0405-7

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