Morten Kam Dahl Dueholm
@mkddueholm
Assoc. Prof. Aalborg University 🇩🇰 Applied microbial ecology with focus on wastewater treatment, anaerobic digestion, and soil. HQ MAGs, transcriptomics, rRNA operon sequencing, culturomics, biofilms, EPS, and functional amyloids.
Another really exciting highlight was that we were able to identify and define two novel Nitrospiraceae genera, Nitrosoma and Nitrocyclum. Both contained conserved nitrite-oxidation genes (nxrAB) and were mainly found in warmer WWTPs.
And genus-level patterns don't tell the whole story. Looking at four important groups of polyphosphate-accumulating organisms, we found clear species-level differences in storage metabolism and denitrification potential. Closely related species can have quite different functional repertoires.
This is important because it allowed us to determine how well genomically encoded traits are conserved across the core genera.
Something we were particularly interested in was connecting this back to MiDAS 4. We recovered MAGs for all 250 core genera identified in our global 16S rRNA survey (248 with HQ MAGs). For the average core genus, we now have 32 independent HQ MAGs!
But does the catalog actually represent the activated sludge microbiome well? The 53,501 MAGs recruited a median of 77.6% of microbial reads from our metagenomes. And in 295 independent activated sludge metagenomes from around the world, the median coverage was 72.8%.
We did quite a bit of sequencing! One PromethION flow cell per sample gave us 11.3 Tbp of long-read data, from which we recovered 53,501 MAGs, including 22,277 high-quality MAGs. The HQ MAGs represent 12,047 species of which 82% are not represented in GTDB r226.
Check out the MiDAS global genome catalog preprint! We applied Nanopore long-read metagenomics to 83 selected samples from the MiDAS 4 global survey of wastewater treatment plants to create a genome catalog covering all core genera in the activated sludge microbiome. www.biorxiv.org/content/10.6...
It is seldom that I get into the lab as a PI. However, today I had to go back to the lab to revive two amyloid-producing strains from my master’s project. They will be used to develop new proteomics methods for detecting amyloids in complex samples.
Finally, we show that the sequencing platform does not bias ASV relative abundances across environments, and that alpha-diversity measures are directly comparable!
Using increasingly complex communities, we demonstrate that the approach is broadly applicable to microbial communities.
Using the ZymoBIOMICS mock community, we show that we can recover perfect ASVs for essentially all theoretical ASVs ranging in size from 250 bp (V4) to 4200 bp (rRNA operons).
Wow, I didn't know dynabeads were that old.🤓 Our master project was carried out in 2018, so a pretty young study compared to yours.
Time to upgrade your 16S_rRNA V4 primers! A thanks to Parada et al. 2018 and Apprill et al. 2015. Welcome Hu et al. 2024. Greatly improved coverage for #Patescibacteria/#CPR with minimal bias on other known taxa. #MicroSky 🦠🧫 microbiomejournal.biomedcentral.com/articles/10....
Microflora Danica: the atlas of Danish environmental microbiomes. What can you learn from sequencing 10,000 metagenomes, and 14.9 million bacterial and 13.4 million eukaryotic rRNA operons?🦠 If you haven't read our preprint, it might be the time now. 😁 www.biorxiv.org/content/10.1...
Time to upgrade your #16S_rRNA V4 primers! Goodbye Parada et al. 2018 and Apprill et al. 2015. Welcome Hu et al. 2023. Greatly improved coverage for #Patescibacteria/CPR with minimal bias on other known taxa. #MicroSky 🦠🧫 www.biorxiv.org/content/10.1...
Today my first PhD student Christina K. Overgaard successfully defended her PhD. 🎉 It has been an honor to work with her as a supervisor, and I wish her all the best of luck in her future endeavors.😁 Also a big thanks to the evaluation committee: Alexander Loy, Søren Sørensen and Teis Søndergaard.
Achieve microbial community profiling superpowers for #wastewater_treatment systems and #anaerobic_digesters with the MiDAS 5 #16S_rRNA_gene reference database. Here is a link to the preprint: www.biorxiv.org/content/10.1...
Excited to finally present: 🌍MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.🦠 The title speaks for itself.🍾🎉 www.biorxiv.org/content/10.1...