How to contact us

Feature requests / bug reports should be submitted via the official GitHub repository.
Questions should be addressed to: Daniel Mende, Georg Zeller or Shinichi Sunagawa.


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

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

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

Microbiome 10, Article number: 212 (2022):

For mOTUs2:

Microbial abundance, activity and population genomic profiling with mOTUs2

Alessio Milanese*, Daniel R Mende*, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis P Coelho, T Sebastian B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller#, Shinichi Sunagawa#.

Nature Communications 10, Article number: 1014 (2019):

For mOTUs1:

Metagenomic species profiling using universal phylogenetic marker genes

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

Nature Methods 10, 1196–1199 (2013):


For more information on how to run mOTUs, see:

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

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

Current Protocols 1, e218 (2021):

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mOTUs v1

The codebase of the first version of mOTUs can be found here.


mOTUs is published under the GPL-3.0 license.