CITATION.cff

cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: 'Microbial abundance, activity and population genomic profiling with mOTUs2'
doi: 10.1038/s41467-019-08844-4
authors:
  - given-names: Alessio
    family-names: Milanese
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-7050-2239
  - given-names: Daniel R.
    family-names: Mende
    affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
    orcid: https://orcid.org/0000-0001-6831-4557
  - given-names: Lucas
    family-names: Paoli
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      & Department of Biology, École normale supérieure, Paris, France
    orcid: https://orcid.org/0000-0003-0771-8309
  - given-names: Guillem
    family-names: Salazar
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0002-9786-1493
  - given-names: Miguelangel
    family-names: Cuenca
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0003-3435-9102
  - given-names: Pascal 
    family-names: Hingamp
    affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
  - given-names: Renato
    family-names: Alves
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-7212-0234
  - given-names: Paul I.
    family-names: Costea
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0003-1645-3947
  - given-names: Luis Pedro
    family-names: Coelho
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-9280-7885
  - given-names: Thomas S. B.
    family-names: Schmidt 
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0001-8587-4177
  - given-names: Alexandre 
    family-names: Almeida 
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
      & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
    orcid: https://orcid.org/0000-0001-8803-0893
  - given-names: Alex L 
    family-names: Mitchell
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
  - given-names: Robert D.
    family-names: Finn
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
    orcid: https://orcid.org/0000-0001-8626-2148
  - given-names: Jaime 
    family-names: Huerta-Cepas
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      & Centro de Biotecnología y Genómica de Plantas, 
      Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
    orcid: https://orcid.org/0000-0003-4195-5025
  - given-names: Peer 
    family-names: Bork
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      & Max Delbrück Centre for Molecular Medicine, Berlin, Germany
      & Molecular Medicine Partnership Unit, Heidelberg, Germany
      & Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
    orcid: https://orcid.org/0000-0002-2627-833X
  - given-names: Georg
    family-names: Zeller
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0003-1429-7485
  - given-names: Sunagawa
    family-names: Shinichi
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0003-3065-0314

version: 3.0.3
date-released: 2022-07-13
repository-code: https://github.com/motu-tool/mOTUs
license: GNU General Public License v3.0
keywords:
- "Metagenomics"
- "Microbiome"
- "Software"
preferred-citation:
  type: article
  authors:
    - given-names: Alessio
      family-names: Milanese
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-7050-2239
    - given-names: Daniel R.
      family-names: Mende
      affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
      orcid: https://orcid.org/0000-0001-6831-4557
    - given-names: Lucas
      family-names: Paoli
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
        & Department of Biology, École normale supérieure, Paris, France
      orcid: https://orcid.org/0000-0003-0771-8309
    - given-names: Guillem
      family-names: Salazar
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0002-9786-1493
    - given-names: Miguelangel
      family-names: Cuenca
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0003-3435-9102
    - given-names: Pascal 
      family-names: Hingamp
      affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
    - given-names: Renato
      family-names: Alves
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-7212-0234
    - given-names: Paul I.
      family-names: Costea
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0003-1645-3947
    - given-names: Luis Pedro
      family-names: Coelho
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-9280-7885
    - given-names: Thomas S. B.
      family-names: Schmidt 
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0001-8587-4177
    - given-names: Alexandre 
      family-names: Almeida 
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
        & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
      orcid: https://orcid.org/0000-0001-8803-0893
    - given-names: Alex L 
      family-names: Mitchell
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
    - given-names: Robert D.
      family-names: Finn
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
      orcid: https://orcid.org/0000-0001-8626-2148
    - given-names: Jaime 
      family-names: Huerta-Cepas
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
        & Centro de Biotecnología y Genómica de Plantas, 
        Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
      orcid: https://orcid.org/0000-0003-4195-5025
    - given-names: Peer 
      family-names: Bork
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
        & Max Delbrück Centre for Molecular Medicine, Berlin, Germany
        & Molecular Medicine Partnership Unit, Heidelberg, Germany
        & Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
      orcid: https://orcid.org/0000-0002-2627-833X
    - given-names: Georg
      family-names: Zeller
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0003-1429-7485
    - given-names: Sunagawa
      family-names: Shinichi
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0003-3065-0314
  doi: "10.1038/s41467-019-08844-4"
  journal: "Nature Communications"
  month: 3
  year: 2019
  title: "Microbial abundance, activity and population genomic profiling with mOTUs2"
  abstract: 'Metagenomic sequencing has greatly improved our ability to profile the composition 
  of environmental and host-associated microbial communities. However, the dependency of most methods 
  on reference genomes, which are currently unavailable for a substantial fraction of microbial species, 
  introduces estimation biases. We present an updated and functionally extended tool 
  based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based 
  operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. 
  As more than 30% of them could not previously be quantified at this taxonomic resolution, 
  relative abundance estimates based on mOTUs are more accurate compared to other methods. 
  As a new feature, we show that mOTUs, which are based on essential housekeeping genes, 
  are demonstrably well-suited for quantification of basal transcriptional activity of community members. 
  Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, 
  which allows for comparing microbial strain populations (e.g., across different human body sites).'