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
Ruscheweyh HJ*, Milanese A*, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G#, Sunagawa S#
Microbiome. 2022 Dec 5;10(1):212. doi:10.1186/s40168-022-01410-z

For mOTUs2:

Microbial abundance, activity and population genomic profiling with mOTUs2
Milanese A*, Mende DR*, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G#, Sunagawa S#
Nat Commun. 2019 Mar 4;10(1):1014. doi:10.1038/s41467-019-08844-4

For mOTUs1:

Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
Nat Methods. 2013 Dec;10(12):1196-9. doi:10.1038/nmeth.2693


For more information on how to run mOTUs, see:

mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities
Ruscheweyh HJ*, Milanese A*, Paoli L, Sintsova A, Mende DR, Zeller G#, Sunagawa S#
Curr Protoc. 2021 Aug;1(8):e218. doi:10.1002/cpz1.218


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


mOTUs is published under the GPL-3.0 license.