Morten Kam Dahl Dueholm
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.
- Reposted by Morten Kam Dahl DueholmNew blog post: ONT read QC strategies for assembly rrwick.github.io/2026/02/05/r... Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
- Reposted by Morten Kam Dahl DueholmKtedonobacteria are so freaking cool, with 10+ Mbp genomes, interesting morphologies and tons of BGCs
- Chromid-like secondary replicons as key sites of biosynthetic gene clusters in Ktedonobacteria biorxiv.org/content/10.64898/20…
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- Reposted by Morten Kam Dahl DueholmAnnouncing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
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- Reposted by Morten Kam Dahl DueholmNew paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...
- Reposted by Morten Kam Dahl DueholmNew paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
- Really important read for people working with long-read MAGs. www.nature.com/articles/s41...
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- Ever wondered if your favorite bacteria 🧫🦠 produce exopolysaccharides? You can now easily check that with epsSMASH, our new bioinformatic tool built on the antiSMASH framework. It detects both known and novel exoPS BGCs. Check out and share the preprint! www.biorxiv.org/content/10.6...
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- Reposted by Morten Kam Dahl Dueholm💾 any2fasta 0.8.1 is released! The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz #bioinformatiocs #microbiology #genomcs github.com/tseemann/any...
- Reposted by Morten Kam Dahl DueholmWith all the excitement about AI giving us answers, we often forget that the real trick is to figure out what is the question.
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- Reposted by Morten Kam Dahl DueholmUseful discussion on circular contigs in metagenome assembly
- Metagenomics colleagues! Anybody know if a good piece of software to test whether Illumina contigs are circular? @antobeck.bsky.social?
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- Once in a while, you publish an article that fundamentally redefines your research area. I believe this is one of those moments. I huge thanks to all contributors. 🎉
- Reposted by Morten Kam Dahl DueholmAll you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
- A scalable transposon mutagenesis system for non-model bacteria biorxiv.org/content/10.64898/20…
- Reposted by Morten Kam Dahl Dueholm⭐NAR Breakthrough! ⭐ 🧬 A synthetic RNA forms a #G-quadruplex without a G-rich sequence, using a complex 3D fold and GTP as a ligand. This suggests G-quadruplexes may be far more widespread in biologically important RNAs. Read more: doi.org/10.1093/nar/... #NARBreaktrhough #RNA #StructuralBiology
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- Reposted by Morten Kam Dahl Dueholm🦠 New #symbionts in #wastewater: #denitrifying #protist #endosymbionts are found in #sewage plants all over the world. One common species releases #nitrousoxide. Our now @isme-microbes.bsky.social mpi-bremen.de/en/Page6579.... doi.org/10.1093/isme... @daanspeth.bsky.social @einzeller.bsky.social
- Reposted by Morten Kam Dahl DueholmNice new review on my favorite topic. www.cell.com/trends/ecolo...
- Reposted by Morten Kam Dahl Dueholm💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...
- Reposted by Morten Kam Dahl DueholmDNA is the best kind of time machine - really feels like we’re in a golden age of big data studies like this. Can’t wait to read!
- New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...
- Reposted by Morten Kam Dahl Dueholm“Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota” by @kohtzarchaeota.bsky.social, Sylvia Nupp, and myself is out in Science Advances. 90% enriched culture of a methyl-dismutating thermoproteotal methanogen. #Microsky 🧪 tinyurl.com/bdcc3uzs
- Reposted by Morten Kam Dahl DueholmDenmark just mapped its entire environmental microbiome. More than 10,000 samples revealing hidden, dominant nitrifiers that shape fertilizer use, water quality, and climate impact. A national microbiome atlas could transform sustainable agriculture across Europe. #AMR www.nature.com/articles/s41...
- Reposted by Morten Kam Dahl DueholmFrom @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓 ⬇️ academic.oup.com/nar/advance-...
- Reposted by Morten Kam Dahl DueholmPhages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh
- Reposted by Morten Kam Dahl DueholmAfter years of struggling with how to cryopreserve one of our endosymbiotic bacteria, we found something that worked! 🦠☃️ We crowd-sourced suggestions and then @ruthwright.bsky.social tried the most common ones (like 🥛...). Want to do the same? Here is how we did it: www.biorxiv.org/content/10.6...
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- New review on the structure and function of bacterial amyloids. My PhD student @andersohd.bsky.social did a great job with the bioinformatic analysis of both curli and Fap amyloids. advanced.onlinelibrary.wiley.com/doi/epdf/10....
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- Reposted by Morten Kam Dahl DueholmRespiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬 Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations! doi.org/10.1093/isme...
- People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding
- Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...
- Protist–bacteria partnerships are more common in wastewater treatment plants than we thought. In this ISME communications paper, we uncovered widespread denitrifying endosymbionts inside ciliates, their global distribution, and their temporal dynamics across WWTPs.🦠 academic.oup.com/ismecommun/a...
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- Reposted by Morten Kam Dahl DueholmExcited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...
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- Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...
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- I had a master student who used the same technique to identify transcription factors associated with functional amyloids in Pseudomonas several years ago. We did not have the man power to confirm our hits using knock out mutants, so we never published the results, but cool technique 😎
- We are organizing a conference on environmental biofilms and EPS in Aalborg, Denmark in April 2026 🦠🧫🧬 All biofilm and EPS enthusiasts should consider to join.👩🔬👨🔬 Please share this invitation with your scientific networks and here! Abstract submission is open until December 8. www.eps26.bio.aau.dk
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- Reposted by Morten Kam Dahl DueholmReally cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
- Reposted by Morten Kam Dahl Dueholmrdcu.be/eRxNf here our new study on the characterization of the lipopolysaccharide holotranslocon, LptDE and the newly identified subunits LptM and LptY. Great collaboration with @fronzeslab.bsky.social @pstansfeld.bsky.social @JulienMarcoux @YvesQuentin
- High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...
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- Reposted by Morten Kam Dahl DueholmOur paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠
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