About and contact#

Team#

Development team:

  • Marija Dmitrijeva (ETH Zurich, Swiss Institute of Bioinformatics)

  • Hans-Joachim Ruscheweyh (ETH Zurich, Swiss Institute of Bioinformatics)

  • Kang Li (ETH Zurich)

  • Lilith Feer (ETH Zurich)

  • Samuel Miravet-Verde (ETH Zurich, Swiss Institute of Bioinformatics)

Support:

  • Georg Zeller (Leiden University Medical Center)

  • Daniel R. Mende (Keio University)

  • Patrick Wörz (Leiden University Medical Center)

  • Taylor Priest (ETH Zurich, Swiss Institute of Bioinformatics)

  • Infrastructure: Institute of Microbiology IT (ETH Zurich)

  • Computation: HPC Group (ETH Zurich)

Lead:

Shinichi Sunagawa (ETH Zurich, Swiss Institute of Bioinformatics)

How to contact us#

We encourage you to join our Discord community to submit questions and feature requests.

Alternatively, you can send an email to microbiomics@ethz.ch.

How to cite us#

If you find the mOTUs genome database useful in your work, please cite:

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities

Dmitrijeva Marija, Ruscheweyh Hans-Joachim, Feer Lilith, Li Kang, Miravet-Verde Samuel, Sintsova Anna, Mende Daniel R, Zeller Georg, Sunagawa Shinichi

Nucleic Acids Research (2024); gkae1004.

To cite previous versions of the profiler:

mOTUs3

Reference genome-independent taxonomic profiling of microbiomes with mOTUs3

Ruscheweyh Hans-Joachim, Milanese Alessio, Paoli Lucas, Karcher Nicolai, Clayssen Quentin, Keller Marisa Isabell, Wirbel Jakob, Bork Peer, Mende Daniel R, Zeller Georg, Sunagawa Shinichi

Microbiome (2022); 10(1):212.

mOTUs2

Microbial abundance, activity and population genomic profiling with mOTUs2

Milanese Alessio, Mende Daniel R, Paoli Lucas, Salazar Guillem, Ruscheweyh Hans-Joachim, Cuenca Miguelangel, Hingamp Pascal, Alves Renato, Costea Paul I, Coelho Luis Pedro, Schmidt Thomas SB, Almeida Alexandre, Mitchell Alex L, Finn Rob D, Huerta-Cepas Jaime, Bork Peer, Zeller Georg, Sunagawa Shinichi

Nature Communications (2019); 10(1):1014

mOTUs1

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa Shinichi, Mende Daniel R, Zeller Georg, Izquierdo-Carrasco Fernando, Berger Simon A, Kultima Jens Roat, Coelho Luis Pedro, Arumugam Manimozhiyan, Tap Julien, Nielsen Henrik Bjørn, Rasmussen Simon, Brunak Søren, Pedersen Oluf, Guarner Francisco, de Vos Willem M, Wang Jun, Li Junhua, Doré Joël, Ehrlich S Dusko, Stamatakis Alexandros, Bork Peer

Nature Methods (2013); 10(12):1196-9.

To cite the protocol paper:

mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities

Ruscheweyh Hans-Joachim, Milanese Alessio, Paoli Lucas, Sintsova Anna, Mende Daniel R, Zeller Georg, Sunagawa Shinichi

Current Protocols (2021); 1(8):e218.

Funding#

ETH Zurich
Swiss Institute for Bioinformatics
Swiss National Science Foundation
NCCR Microbiomes

Data provenance#

source_data Overview of data sources used to collect reference genomes and shotgun metagenomes for mOTUs-db.

mgdb The mOTUs4 marker gene database.

annotationdb The mOTUs4 functional annotation database.

Licensing and privacy policy#

License: GPL-3 The mOTUs tool code is open source and released under the GPL-3 license.

License: CC BY 4.0 Genome sequences and associated data are released under the CC-BY 4.0 license

mOTUs follows SIB’s privacy policy.

ico1 mOTUs is part of SIB's portfolio of open tools and databases.

ico2 mOTUs is part of the ELIXIR-CH Service Delivery Plan.