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    DOI10.15468/33qqsm

    Occurrence dataset Registered April 30, 2025

    Microflora Danica: Bacterial 16S rRNA genes (UMIs)

    Published by Department of Chemistry and Bioscience, Aalborg University
    21 authors
    github.com
    LicenceCC BY 4.0

    Description

    This project contains the near full-length UMI 16S rRNA gene data belonging to the Microflora Danica project. The Microflora Danica project encompasses over 10,000 samples from across Denmark, taken between 2019 and 2023 with the goal to cover as much of the microbial diversity in the investigated habitats as possible. For the bacterial and eukaryotic operon data see https://doi.org/10.15468/yr5rmw and https://doi.org/10.15468/ea7jvq, respectively.

    The unique molecular identifiers (UMIs) approach relies on the use of molecular nucleotide template tagging to achieve high-accuracy single-molecule consensus calling on the Oxford Nanopore sequencing platform. The addition of UMIs to both ends of the template enables the bioinformatic identification and removal of chimeras formed during PCR.

    In the project the UMI 16S rRNA gene sequences was used together with near full-length 16S rRNA gene sequences to construct the Microflora Danica 16S rRNA gene reference database (https://zenodo.org/records/12605769) and to investigate the 16S rRNA gene sequence diversity and novelty of species representative sequences. Furthermore, the UMI 16S rRNA gene data was solely used for the estimation of the bacterial richness of the Danish terrestrial habitats and in the analysis of different diversity metrics in the manuscript (https://doi.org/10.1101/2024.06.27.600767).

    Funding was provided by the Poul Due Jensen/Grundfos Foundation.
    Associated metadata is also available from github (https://github.com/cmc-aau/mfd_wiki).

    [This dataset was processed using the GBIF Metabarcoding Data Toolkit.]

    Metrics

    Bibliography

    • Microflora Danica: the atlas of Danish environmental microbiomes CM Singleton, TBN Jensen, F Delogu, EA Sørensen, VR Jørgensen, SM Karst, Y Yang, KS Knudsen, M Sereika, F Petriglieri, S Knutsson, SM Dall, RH Kirkegaard, JM Kristensen, BJ Woodcroft, DR Speth, STN Aroney, The Microflora Danica Consortium, M Wagner, MKD Dueholm, PH Nielsen, M Albertsen
      Identifier: DOI:https://doi.org/10.1101/2024.06.27.600767Google Scholar

    Contacts

    • Thomas B N Jensen

      Originator
      Administrative point of contact
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      Administrative point of contact
      User ID

    • Caitlin M Singleton

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Francesco Delogu

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Emil A Sørensen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Vibeke R Jørgensen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Søren M Karst

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Kalinka S Knudsen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Mantas Sereika

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Christina K Overgaard

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator

    • Francesca Petriglieri

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Simon Knutsson

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator

    • Sebastian M Dall

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Rasmus H Kirkegaard

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Jannie M Kristensen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Ben J Woodcroft

      Originator
      Organization
      Centre for Microbiome Research, Queensland University of Technology (QUT), Woolloongabba, Australia
      Roles
      Originator
      User ID

    • Daan R Speth

      Originator
      Organization
      Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
      Roles
      Originator
      User ID

    • Samuel T N Aroney

      Originator
      Organization
      Centre for Microbiome Research, Queensland University of Technology (QUT), Woolloongabba, Australia
      Roles
      Originator
      User ID

    • Michael Wagner

      Originator
      Organization
      Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria and Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Morten K D Dueholm

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Per H Nielsen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Mads Albertsen

      Originator
      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      Roles
      Originator
      User ID

    • Henning C Thomsen

      Organization
      Department of Agroecology, Aarhus University, Tjele, Denmark

    • Bent T Christensen

      Organization
      Department of Agroecology, Aarhus University, Tjele, Denmark

    • Lis W de Jonge

      Organization
      Department of Agroecology, Aarhus University, Tjele, Denmark
      User ID

    • Anne-Cathrine S Danielsen

      Organization
      Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University , Tjele, Denmark and Center for Sustainable Landscapes under Global Change, Aarhus, Denmark
      User ID

    • Cecilie Hermansen

      Organization
      Department of Agroecology, Aarhus University, Tjele, Denmark
      User ID

    • Mogens H Greve

      Organization
      Department of Agroecology, Aarhus University, Tjele, Denmark
      User ID

    • Rasmus Ejrnæs

      Organization
      Department of Ecoscience, Aarhus University, Aarhus, Denmark
      User ID

    • Signe Normand

      Organization
      Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University and Center for Sustainable Landscapes under Global Change, Aarhus, Denmark
      User ID

    • Urs A Treier

      Organization
      Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University and Center for Sustainable Landscapes under Global Change, Aarhus, Denmark
      User ID

    • Bjarke Madsen

      Organization
      Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University and Center for Sustainable Landscapes under Global Change, Aarhus, Denmark
      User ID

    • Andreas Schramm

      Organization
      Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Ian P G Marshall

      Organization
      Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Ann-Sofie Dam

    • Kasper U Kjeldsen

      Organization
      Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Kai Finster

      Organization
      Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Philip F Thomsen

      Organization
      Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Eva E Sigsgaard

      Organization
      Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Martin J Klepke

      Organization
      Department of Biology, Aarhus University, Aarhus, Denmark
      User ID

    • Marie Vestergård

      Organization
      Department of Biology, Aarhus University, Aarhus, Denmark

    • Erik Aude

      Organization
      Habitatvision, Lystrup, Denmark

    • Lene Thomsen

      Organization
      Habitatvision, Lystrup, Denmark

    • Camilla Lemming

      Organization
      SEGES Innovation P/S, Aarhus, Denmark

    • Rita Hørfarter

      Organization
      SEGES Innovation P/S, Aarhus, Denmark

    • Marlene M Jensen

      Organization
      Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
      User ID

    • Tobias G Frøslev

      Organization
      Global Biodiversity Information Facility, Denmark
      User ID

    • Lone Gram

      Organization
      DTU Department of Biotechnology and Biomedicine, & Center for Microbial Secondary Metabolits , Kgs. Lyngby, Denmark
      User ID

    • Peter B Svendsen

      Organization
      DTU Department of Biotechnology and Biomedicine, & Center for Microbial Secondary Metabolits , Kgs. Lyngby, Denmark
      User ID

    • Morten D Schostag

      Organization
      DTU Department of Biotechnology and Biomedicine, & Center for Microbial Secondary Metabolits , Kgs. Lyngby, Denmark
      User ID

    • Sanne Kjellerup

      Organization
      WSP Danmark A/S, Tåstrup, Denmark

    • Torben L Skovhus

      Organization
      Research centre for built environment, climate and water technology, VIA University College, Horsens, Denmark
      User ID

    • Ditte A Søborg

      Organization
      Research centre for built environment, climate and water technology, VIA University College, Horsens, Denmark
      User ID

    • Kasper R Jensen

      Organization
      Department of Biology, University of Southern Denmark, Odense, Denmark
      User ID

    • Jørgen F Pedersen

      Organization
      Skalhuse, Nibe, Denmark

    • Andrew Giguere

      Organization
      Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
      User ID

    • Inge S Pedersen

      Organization
      Department of Molecular Diagnostics, Aalborg University Hospital and Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
      User ID

    • Mads Sønderkær

      Organization
      Department of Molecular Diagnostics, Aalborg University Hospital and Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
      User ID

    • Thomas A Davidson

      Organization
      Department of Ecoscience, Aarhus University, Aarhus, Denmark
      User ID

    • Jes Vollertsen

      Organization
      Department of the Built Environment, Aalborg University, Aalborg, Denmark
      User ID

    • Fan Liu

      Organization
      Department of the Built Environment, Aalborg University, Aalborg, Denmark
      User ID

    • Peter Roslev

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Niels Iversen

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Kåre L Nielsen

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Nadieh de Jonge

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Dan Bruhn

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Jeppe L Nielsen

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Torsten N Kristensen

      Organization
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Marta A Nierychlo

      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
      User ID

    • Giulia Dottorini

      Organization
      Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark

    GBIF registration

    Registration date
    April 30, 2025
    Metadata last modified
    May 27, 2025
    Publication date
    May 27, 2025
    Hosted by
    Danish Biodiversity Information Facility
    Installation
    GBIF Denmark (DanBIF) Metabarcoding Datasets
    Endpoints
    BIOM 2.1
    BIOM 1.0
    Darwin Core Archive
    Preferred identifier
    10.15468/33qqsm
    GBIF registration details

    Citation

    Jensen T B N, Singleton C M, Delogu F, Sørensen E A, Jørgensen V R, Karst S M, Knudsen K S, Sereika M, Overgaard C K, Petriglieri F, Knutsson S, Dall S M, Kirkegaard R H, Kristensen J M, Woodcroft B J, Speth D R, Aroney S T N, Wagner M, Dueholm M K D, Nielsen P H, Albertsen M (2025). Microflora Danica: Bacterial 16S rRNA genes (UMIs). Department of Chemistry and Bioscience, Aalborg University. Occurrence dataset https://doi.org/10.15468/33qqsm accessed via GBIF.org on 2025-08-15.