Morten Kam Dahl Dueholm
@mkddueholm.bsky.social
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 Dueholm
Identification of Previously Unknown DNA-Binding Proteins Using DNA Affinity/Pull-Down Methods Followed by Mass Spectrometry
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
November 26, 2025 at 4:00 PM
Identification of Previously Unknown DNA-Binding Proteins Using DNA Affinity/Pull-Down Methods Followed by Mass Spectrometry
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
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 😎
Identification of Previously Unknown DNA-Binding Proteins Using DNA Affinity/Pull-Down Methods Followed by Mass Spectrometry
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson
Current Protocols 2025, 5:e70264
doi: 10.1002/cpz1.70264
#MicroSky
November 26, 2025 at 7:44 PM
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
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
Conference: Environmental biofilms: matrix composition, properties and applications
Conference:
Environmental biofilms: matrix composition, properties and applications
www.eps26.bio.aau.dk
November 26, 2025 at 2:37 PM
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
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
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications
The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...
www.nature.com
November 25, 2025 at 1:44 PM
Really 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 Dueholm
rdcu.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
Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex
Nature Communications - The asymmetric distribution of lipopolysaccharide (LPS) on the surface of the bacterial outer membrane is essential and crucial for antibiotic resistance. Here, authors...
rdcu.be
November 24, 2025 at 4:08 PM
rdcu.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...
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules
Abstract. Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most m
academic.oup.com
November 25, 2025 at 8:56 AM
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...
Reposted by Morten Kam Dahl Dueholm
We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! New PhD and PostDoc positions in my lab at Aalborg University
November 24, 2025 at 8:49 PM
We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! New PhD and PostDoc positions in my lab at Aalborg University
Reposted by Morten Kam Dahl Dueholm
Our 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
🖥️🧬🦠
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
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our 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
🖥️🧬🦠
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
🖥️🧬🦠
Reposted by Morten Kam Dahl Dueholm
🧬🖥️SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
Abstract. Since 2007, the SILVA database (https://www.arb-silva.de/) has served as a comprehensive resource providing quality-checked, aligned, and classif
academic.oup.com
November 19, 2025 at 10:36 AM
🧬🖥️SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
Reposted by Morten Kam Dahl Dueholm
Clone-FISH paper out: Manuscript/resource alert #microsky 🦠 We present a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 17 yet uncultured ones.
November 17, 2025 at 2:36 PM
Clone-FISH paper out: Manuscript/resource alert #microsky 🦠 We present a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 17 yet uncultured ones.
Reposted by Morten Kam Dahl Dueholm
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology
Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.
www.nature.com
November 5, 2025 at 3:34 PM
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Reposted by Morten Kam Dahl Dueholm
Version 5.1.1 of the PR2 database has been released.
The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations
The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity
Abstract. Metabarcoding has emerged as a robust method for assessing biodiversity patterns by retrieving environmental DNA directly from ecosystems. While
doi.org
October 28, 2025 at 8:59 AM
Version 5.1.1 of the PR2 database has been released.
The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations
The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations
Reposted by Morten Kam Dahl Dueholm
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Morten Kam Dahl Dueholm
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
October 21, 2025 at 6:25 PM
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
Reposted by Morten Kam Dahl Dueholm
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 5:08 PM
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
Reposted by Morten Kam Dahl Dueholm
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 1:38 PM
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Reposted by Morten Kam Dahl Dueholm
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles
peercommunityjournal.org
October 18, 2025 at 7:58 AM
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
Reposted by Morten Kam Dahl Dueholm
Fascinating Evo mechanism: diversity-generating retroelements (DGRs)! Highly abundant and frequently horizontally transferred - diversifying ligand-binding domains in gut Bacteroides! 🧪🦠 #microsky #microbiomesky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...
www.science.org
October 11, 2025 at 2:52 PM
Fascinating Evo mechanism: diversity-generating retroelements (DGRs)! Highly abundant and frequently horizontally transferred - diversifying ligand-binding domains in gut Bacteroides! 🧪🦠 #microsky #microbiomesky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation - Nature Microbiology
Opposing forces generated by exopolysaccharide trail binding versus type IV pilus retraction generate a high cyclic diGMP–high cyclic AMP state in Pseudomonas aeruginosa that promotes social motility.
www.nature.com
October 9, 2025 at 9:20 PM
Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Morten Kam Dahl Dueholm
metaPR2 version 3.0 has just been released.
Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.
app.metapr2.org
Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.
app.metapr2.org
MetaPR2
app.metapr2.org
October 6, 2025 at 3:28 PM
metaPR2 version 3.0 has just been released.
Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.
app.metapr2.org
Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.
app.metapr2.org
Reposted by Morten Kam Dahl Dueholm
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation
-in Science Advances from Ümit Akbey
with @mkddueholm.bsky.social
www.science.org/doi/10.1126/...
-in Science Advances from Ümit Akbey
with @mkddueholm.bsky.social
www.science.org/doi/10.1126/...
Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation
The structure of FapC reveals how Pseudomonas forms biofilms via a unique β solenoid amyloid fold and dynamic assembly pathway.
www.science.org
September 28, 2025 at 2:06 PM
Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation
-in Science Advances from Ümit Akbey
with @mkddueholm.bsky.social
www.science.org/doi/10.1126/...
-in Science Advances from Ümit Akbey
with @mkddueholm.bsky.social
www.science.org/doi/10.1126/...
Reposted by Morten Kam Dahl Dueholm
