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Microbial abundance, activity and population genomic profiling with mOTUs2

Author

Listed:
  • Alessio Milanese

    (European Molecular Biology Laboratory)

  • Daniel R Mende

    (University of Hawaiʻi at Mānoa)

  • Lucas Paoli

    (ETH Zürich
    École normale supérieure)

  • Guillem Salazar

    (ETH Zürich)

  • Hans-Joachim Ruscheweyh

    (ETH Zürich)

  • Miguelangel Cuenca

    (ETH Zürich)

  • Pascal Hingamp

    (Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110)

  • Renato Alves

    (European Molecular Biology Laboratory
    Candidate for Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences)

  • Paul I Costea

    (European Molecular Biology Laboratory)

  • Luis Pedro Coelho

    (European Molecular Biology Laboratory)

  • Thomas S. B. Schmidt

    (European Molecular Biology Laboratory)

  • Alexandre Almeida

    (European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus
    Wellcome Trust Sanger Institute, Wellcome Genome Campus)

  • Alex L Mitchell

    (European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus)

  • Robert D. Finn

    (European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus)

  • Jaime Huerta-Cepas

    (European Molecular Biology Laboratory
    Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM)

  • Peer Bork

    (European Molecular Biology Laboratory
    Max Delbrück Centre for Molecular Medicine
    Molecular Medicine Partnership Unit
    University of Würzburg)

  • Georg Zeller

    (European Molecular Biology Laboratory)

  • Shinichi Sunagawa

    (ETH Zürich)

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).

Suggested Citation

  • Alessio Milanese & Daniel R Mende & Lucas Paoli & Guillem Salazar & Hans-Joachim Ruscheweyh & Miguelangel Cuenca & Pascal Hingamp & Renato Alves & Paul I Costea & Luis Pedro Coelho & Thomas S. B. Schm, 2019. "Microbial abundance, activity and population genomic profiling with mOTUs2," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08844-4
    DOI: 10.1038/s41467-019-08844-4
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    Cited by:

    1. Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Vincent Somerville & Nadine Thierer & Remo S. Schmidt & Alexandra Roetschi & Lauriane Braillard & Monika Haueter & Hélène Berthoud & Noam Shani & Ueli Ah & Florent Mazel & Philipp Engel, 2024. "Genomic and phenotypic imprints of microbial domestication on cheese starter cultures," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Svetlana Kutuzova & Mads Nielsen & Pau Piera & Jakob Nybo Nissen & Simon Rasmussen, 2024. "Taxometer: Improving taxonomic classification of metagenomics contigs," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    4. Trine Zachariasen & Jakob Russel & Charisse Petersen & Gisle A. Vestergaard & Shiraz Shah & Pablo Atienza Lopez & Moschoula Passali & Stuart E. Turvey & Søren J. Sørensen & Ole Lund & Jakob Stokholm &, 2024. "MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Rocky D. Payet & Lorelei J. Bilham & Shah Md Tamim Kabir & Serena Monaco & Ash R. Norcott & Mellieha G. E. Allen & Xiao-Yu Zhu & Anthony J. Davy & Charles A. Brearley & Jonathan D. Todd & J. Benjamin , 2024. "Elucidation of Spartina dimethylsulfoniopropionate synthesis genes enables engineering of stress tolerant plants," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Corentin Hochart & Lucas Paoli & Hans-Joachim Ruscheweyh & Guillem Salazar & Emilie Boissin & Sarah Romac & Julie Poulain & Guillaume Bourdin & Guillaume Iwankow & Clémentine Moulin & Maren Ziegler & , 2023. "Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Suguru Nishijima & Naoyoshi Nagata & Yuya Kiguchi & Yasushi Kojima & Tohru Miyoshi-Akiyama & Moto Kimura & Mitsuru Ohsugi & Kohjiro Ueki & Shinichi Oka & Masashi Mizokami & Takao Itoi & Takashi Kawai , 2022. "Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Laura Nies & Susheel Bhanu Busi & Mina Tsenkova & Rashi Halder & Elisabeth Letellier & Paul Wilmes, 2022. "Evolution of the murine gut resistome following broad-spectrum antibiotic treatment," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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