Microflora DanicaScopeMicroflora Danica (MFD) is set to create the compendium of the microbial populations of Denmark using 10.000+ metagenomic samples encompassing soils, waters and sediments from natural, agricultural and built environments.More than 50 subprojects are included in MFD, with various degrees of spatial resolutions, depth of associated data and technical challenges. This wiki is meant to help the researchers in navigating the various subprojects, data and results from MFD.The first flagship manuscript "Microflora Danica: the atlas of Danish environmental microbiomes" is available as a preprint on bioRxiv. The data are publicly available, its findings can be explored and reproduced starting from The MFD Atlas page of this wiki.IntroductionMicroflora Danica is the Atlas of the enviromental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 412 near full-length 16S UMI datasets and 450 bacterial and eukaryotic rRNA operon collections, linked to a detailed 5-level habitat ontology. The manuscript determines that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.DataThis project encompasses additional data files belonging to the Microflora Danica project. Here we deopisted:Metagenomic assemblies.Metagenome bins (MQ MAGs). The MFG (Microflora Global) 16S rRNA gene reference database (unclustered and clustered at 98.7% ANI).Metagenomic derived 16S rRNA gene fragments derived from the 10km reference grid representative samples.Genus-aggregated observational tables of the 16S rRNA gene fragments (counts and relative abundance) as well as versions of these subjected to random subsampling without replacement.OTU tables of the 16S UMI, 16S and 18S sequences from operons. Data used in the analysis for evaluation of the effect of drying performed for the agricultural samples. Supplementary data for nitrifier analysis (including packages for GraftM).Supplementary data for metagenomic marker gene analysis (including package for SingleM). Other resourcesThe sequencing data, and metagenome bins (HQ MAGs, >90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).The near-full length 16S UMI as well as the near-full length 16S and 18S from the bacterial and eukaryotic operons has also been deposited in GBIF. This project is supported by the Poul Due Jensen/Grundfos foundation.

Microflora DanicaScopeMicroflora Danica (MFD) is set to create the compendium of the microbial populations of Denmark using 10.000+ metagenomic samples encompassing soils, waters and sediments from natural, agricultural and built environments.More than 50 subprojects are included in MFD, with various degrees of spatial resolutions, depth of associated data and technical challenges. This wiki is meant to help the researchers in navigating the various subprojects, data and results from MFD.The first flagship manuscript "Microflora Danica: the atlas of Danish environmental microbiomes" is available as a preprint on bioRxiv. The data are publicly available, its findings can be explored and reproduced starting from The MFD Atlas page of this wiki.IntroductionMicroflora Danica is the Atlas of the enviromental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 412 near full-length 16S UMI datasets and 450 bacterial and eukaryotic rRNA operon collections, linked to a detailed 5-level habitat ontology. The manuscript determines that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.DataThis project encompasses additional data files belonging to the Microflora Danica project. Here we deopisted:Metagenomic assemblies.Metagenome bins (MQ MAGs). The MFG (Microflora Global) 16S rRNA gene reference database (unclustered and clustered at 98.7% ANI).Metagenomic derived 16S rRNA gene fragments derived from the 10km reference grid representative samples.Genus-aggregated observational tables of the 16S rRNA gene fragments (counts and relative abundance) as well as versions of these subjected to random subsampling without replacement.OTU tables of the 16S UMI, 16S and 18S sequences from operons. Data used in the analysis for evaluation of the effect of drying performed for the agricultural samples. Supplementary data for nitrifier analysis (including packages for GraftM).Supplementary data for metagenomic marker gene analysis (including package for SingleM). Other resourcesThe sequencing data, and metagenome bins (HQ MAGs, >90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).The near-full length 16S UMI as well as the near-full length 16S and 18S from the bacterial and eukaryotic operons has also been deposited in GBIF. This project is supported by the Poul Due Jensen/Grundfos foundation.

Microflora DanicaScopeMicroflora Danica (MFD) is set to create the compendium of the microbial populations of Denmark using 10.000+ metagenomic samples encompassing soils, waters and sediments from natural, agricultural and built environments.More than 50 subprojects are included in MFD, with various degrees of spatial resolutions, depth of associated data and technical challenges. This wiki is meant to help the researchers in navigating the various subprojects, data and results from MFD.The first flagship manuscript "Microflora Danica: the atlas of Danish environmental microbiomes" is available as a preprint on bioRxiv. The data are publicly available, its findings can be explored and reproduced starting from The MFD Atlas page of this wiki.IntroductionMicroflora Danica is the Atlas of the enviromental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 412 near full-length 16S UMI datasets and 450 bacterial and eukaryotic rRNA operon collections, linked to a detailed 5-level habitat ontology. The manuscript determines that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.DataThis project encompasses additional data files belonging to the Microflora Danica project. Here we deopisted:Metagenomic assemblies.Metagenome bins (MQ MAGs). The MFG (Microflora Global) 16S rRNA gene reference database (unclustered and clustered at 98.7% ANI).Metagenomic derived 16S rRNA gene fragments derived from the 10km reference grid representative samples.Genus-aggregated observational tables of the 16S rRNA gene fragments (counts and relative abundance) as well as versions of these subjected to random subsampling without replacement.OTU tables of the 16S UMI, 16S and 18S sequences from operons. Data used in the analysis for evaluation of the effect of drying performed for the agricultural samples. Supplementary data for nitrifier analysis (including packages for GraftM).Supplementary data for metagenomic marker gene analysis (including package for SingleM). Other resourcesThe sequencing data, and metagenome bins (HQ MAGs, >90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).The near-full length 16S UMI as well as the near-full length 16S and 18S from the bacterial and eukaryotic operons has also been deposited in GBIF. This project is supported by the Poul Due Jensen/Grundfos foundation.

Microflora DanicaScopeMicroflora Danica (MFD) is set to create the compendium of the microbial populations of Denmark using 10.000+ metagenomic samples encompassing soils, waters and sediments from natural, agricultural and built environments.More than 50 subprojects are included in MFD, with various degrees of spatial resolutions, depth of associated data and technical challenges. This wiki is meant to help the researchers in navigating the various subprojects, data and results from MFD.The first flagship manuscript "Microflora Danica: the atlas of Danish environmental microbiomes" is available as a preprint on bioRxiv. The data are publicly available, its findings can be explored and reproduced starting from The MFD Atlas page of this wiki.IntroductionMicroflora Danica is the Atlas of the enviromental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 412 near full-length 16S UMI datasets and 450 bacterial and eukaryotic rRNA operon collections, linked to a detailed 5-level habitat ontology. The manuscript determines that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.DataThis project encompasses additional data files belonging to the Microflora Danica project. Here we deopisted:Metagenomic assemblies.Metagenome bins (MQ MAGs). The MFG (Microflora Global) 16S rRNA gene reference database (unclustered and clustered at 98.7% ANI).Metagenomic derived 16S rRNA gene fragments derived from the 10km reference grid representative samples.Genus-aggregated observational tables of the 16S rRNA gene fragments (counts and relative abundance) as well as versions of these subjected to random subsampling without replacement.OTU tables of the 16S UMI, 16S and 18S sequences from operons. Data used in the analysis for evaluation of the effect of drying performed for the agricultural samples. Supplementary data for nitrifier analysis (including packages for GraftM).Supplementary data for metagenomic marker gene analysis (including package for SingleM). Other resourcesThe sequencing data, and metagenome bins (HQ MAGs, >90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).The near-full length 16S UMI as well as the near-full length 16S and 18S from the bacterial and eukaryotic operons has also been deposited in GBIF. This project is supported by the Poul Due Jensen/Grundfos foundation.

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. For 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. 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). DISCLAIMER: 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: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.]

This project contains the near full-length 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 16S UMI rRNA gene data and eukaryotic operon data see https://doi.org/10.15468/33qqsm and https://doi.org/10.15468/ea7jvq, respectively. 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). DISCLAIMER: The 16S rRNA gene data from the bacterial operons should be used for investigation of occurrence only, and are not fit for analysis of diversity metrics: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.]

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.]

This project encompasses additional data files belonging to the Microflora Danica project. The Microflora Danica project encompasses over 10,000 samples from across Denmark, taken between 2019 and 2023 and capturing the habitat types. It provides a reference database of all the microorganisms found in Denmark.The sequencing data, and metagenome bins (>90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).This project is supported by the Poul Due Jensen/Grundfos foundation.

Source data and code (R and Julia) to accompany the paper "Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria".

Source data and code (R and Julia) to accompany the paper "Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria".