This project contains the near full-length 18S 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. \nFor the bacterial 16S UMI rRNA gene data and bacterial operon data see https://doi.org/10.15468/33qqsm and https://doi.org/10.15468/yr5rmw , respectively. \n\nIn 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). \n\nDISCLAIMER: The 18 rRNA gene data from the bacterial operons should be used for investigation of occurrence only, and are not fit for analysis of diversity metrics:\n\nFunding was provided by the Poul Due Jensen/Grundfos Foundation.\nAssociated metadata is also available from github (https://github.com/cmc-aau/mfd_wiki).
[This dataset was processed using the GBIF Metabarcoding Data Toolkit.]
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Danica: the atlas of Danish environmental microbiomes\nCM 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/10.1101/2024.06.27.600767","citationProvidedBySource":false}],"curatorialUnits":[],"taxonomicCoverages":[],"geographicCoverages":[],"temporalCoverages":[],"keywordCollections":[{"thesaurus":"N/A","keywords":["metabarcoding","DNA","MDT"]}],"project":{"title":"Microflora Danica","identifier":"PRJNA1071982","funding":"Funding was provided by the Poul Due Jensen Foundation, PDJF (grant MicroFlora Danica to MA and PHN), Villum Foundation (grant 15510 and 50093 to MA, grant 13351 to PHN), the European Union (ERC grant 101078234 to MA), the Velux Foundation (Grant 21517 to PFT), the Carlsberg Foundation (Grant CF18-0949 to PFT). CMS was supported by a Novo Nordisk Foundation Postdoctoral Fellowship grant (NNF20OC0065005). DS and MW were supported by the Cluster of Excellence grant “Microbiomes drive Planetary Health” of the Austrian Science Fund FWF (10.55776/COE7). SA was supported by the EMERGE National Science Foundation (NSF) Biology Integration Institute (2022070). BW was supported by an Australian Research Council Future Fellowship (FT210100521). This study is funded by the European Union Horizon Europe research and innovation program under Grant agreement No. 101086179 (AI4SoilHealth). Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","awards":[],"relatedProjects":[],"abstract":"In 1752, King Frederik V of Denmark, in line with the historical context of the Age of Enlightenment, commissioned the Flora Danica project to Georg C. Oeder, initiating an “Opus Incomparibile” that took 122 years and produced one of the world’s most unique works in natural history. The resulting atlas included 3000 botanic engravings of flowers and plants over 17 volumes. In 2019, we initiated the Microflora Danica (MFD) project with the aim of cataloguing the microbiomes of Denmark.\n\nMicroflora Danica is the Atlas of the environmental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 420 near-full length UMI 16S rRNA and 450 bacterial and eukaryotic operon datasets. 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