RT @VSelskab: 💥 PODCASTEN GRUNDTANKER er tilbage!. Og vi lægger stærkt ud med @MadsAlbertsen85, der i 1. episode af sæson 4 tager os med på….

RT @kirk3gaard: The dream is to go deep @nanopore on all 10k samples. So far we have done a "pilot" study with 150 samples at 100+Gbp @nano….

RT @kirk3gaard: At #isme19? Today is your chance to catch @SorenHeidelbach present on the epi(c) information that you can get from your @na….

RT @kirk3gaard: At #isme19? Make sure you catch @KnudsenKalinka presenting on the #MicroFloraDanica project today! 10k samples spanning De….

@CaitySing Finally, we are grateful for the generous funding enabling us to make Microflora Danica. The Grundfos Foundation (@PDJF_dk) funding "Microflora Danica" and the Villum Foundation (@VILLUMFONDEN) funding much of the method development before and during the project. 26/26.

@CaitySing Furthermore, the project was enabled by the "Microflora Danica consortium" that supplied samples and habitat classification. We are extremely grateful for their support and collaboration! 25/

This manuscript was spearheaded by Caitlin Singleton (@CaitySing) and Thomas BN Jensen, who both were forces of Nature to make sure everything came together in the end! Several more specific manuscripts are underway! 24/.

This project has been a huge undertaking and so many people have contributed over the years. During covid-19 the Microflora Danica project was even paused for 1.5 years as we pivoted to head the National SARS-CoV-2 sequencing for DK - (Covid-flora Danica?). 23/.

Our deep-dive into Nitrifiers serves as an example of what is possible with the MFD dataset. If you have a favorite organism or functional group you can now investigate their biogeography at unprecedented resolution! All data and metadata is online now! - check the manuscript 22/.

Based on improved HHMs, we screened our 10,686 metagenomes for abundance of AOA, AOB, NOB, and CMX and show that the abundant Nitrifiers are likely not the ones we thought! But, you'll have to read the paper to find out which! 21/

First we used HMM models for amoA and nxr to screen for putative AOA, AOB, NOB, and CMX in our 19,253 assembled MAGs and public genomes. Then manual curation to identify those with relevant complete pathways to be Nitrifiers. (so much work! look at the sup. note 5 and 6. ) 20/.

3) In a land dominated by agriculture, which microbes are involved in Nitrification? 19/.

We combined GTDB with public collections (167,284 "species" genomes) and show that, in most habitats, only 4-8% of species are known on genome level. However, assembling and binning the 10,686 MFD metagenomes to MAGs, doubled the amount of reads attributed to known species. 18/

2) How representative is the global genome databases of the species in Danish habitats? 17/.

Mostly. Microbes follow the environmental gradients, but seem in general (at our resolution) to be broadly distributed if no extreme env. niche selection is present. Hence, using microbes might be a way of supplementing habitat monitoring efforts in the future. 16/

1) Do habitats, largely defined based on macroflora, also reflect distinct microbial niches? 15/.

Having sequenced 10,686 representative samples from Denmark, curated a high-resolution 5-level habitat ontology, and an extremely comprehensive 16S rRNA database we focused on a few questions. 14/.

Finally, we used Illumina shotgun metagenome sequencing on all 10,686 samples, generating approx. 50,000,000,000,000 bp of sequencing data. At this scale, library preparation dominates cost, hence we cut that a factor of 5 by downscaling reactions: 13/.

(we hope some of the large rRNA database initiatives absorb our data quickly, although we know that scaling up raw data a factor 10+ is not without challenges. @ARB_SILVA, GreenGenes (@mcdonadt), @PR2database, EUKARYOME (@tedersoo)) 12/.

To enable bacterial taxonomic classification we merged our previous full-length 16S rRNA sequencing efforts in the Earth Microbiome, American Gut, and Global Wastewater with SILVA to create the Microflora Global database of 350,815 species with a 7-level taxonomy string. 11/.