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
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
Reposted by Morten Kam Dahl Dueholm
Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4
rdcu.be/eH8tr
rdcu.be/eH8tr
Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH
Nature Communications - Rhizosphere microbiomes are shaped by root exudation of diverse organic compounds. Here, the rhizoSMASH algorithm is introduced, which maps microbial genes involved in their...
rdcu.be
September 25, 2025 at 12:07 PM
Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4
rdcu.be/eH8tr
rdcu.be/eH8tr
Reposted by Morten Kam Dahl Dueholm
#NewResearch
Structure of a functional archaellum in bacteria of the Chloroflexota phylum
#MicroSky
@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social @sgribaldo.bsky.social
www.nature.com/articles/s41...
Structure of a functional archaellum in bacteria of the Chloroflexota phylum
#MicroSky
@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social @sgribaldo.bsky.social
www.nature.com/articles/s41...
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology
Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.
www.nature.com
September 22, 2025 at 3:33 PM
#NewResearch
Structure of a functional archaellum in bacteria of the Chloroflexota phylum
#MicroSky
@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social @sgribaldo.bsky.social
www.nature.com/articles/s41...
Structure of a functional archaellum in bacteria of the Chloroflexota phylum
#MicroSky
@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social @sgribaldo.bsky.social
www.nature.com/articles/s41...
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
#News&Views
A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses
www.nature.com/articles/s41...
#microsky
A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses
www.nature.com/articles/s41...
#microsky
A nitrogen-fixing bacterium forms symbioses on land and at sea - Nature Microbiology
Discovery of a marine diatom-associated Bradyrhizobium that nodulates a terrestrial legume expands our understanding of the environmental and host range of nitrogen-fixing symbioses.
www.nature.com
September 18, 2025 at 9:40 AM
#News&Views
A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses
www.nature.com/articles/s41...
#microsky
A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses
www.nature.com/articles/s41...
#microsky
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
Behind the Paper by Michaela M Salcher
Why cultivation still matters in microbiology
communities.springernature.com/posts/why-cu...
Why cultivation still matters in microbiology
communities.springernature.com/posts/why-cu...
Why cultivation still matters in microbiology
The majority of aquatic microbes are still uncultivated. Here, we cultivated 627 strains of abundant freshwater bacteria from 14 lakes, thus generating a collection that includes many previously uncul...
communities.springernature.com
September 2, 2025 at 8:58 AM
Behind the Paper by Michaela M Salcher
Why cultivation still matters in microbiology
communities.springernature.com/posts/why-cu...
Why cultivation still matters in microbiology
communities.springernature.com/posts/why-cu...
Reposted by Morten Kam Dahl Dueholm
Reposted by Morten Kam Dahl Dueholm
Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com!
Read all about it here: nature.com/articles/s41...
Great collab with Chew and Hirao lab
x.com/NiranjanTW/s...
Read all about it here: nature.com/articles/s41...
Great collab with Chew and Hirao lab
x.com/NiranjanTW/s...
Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning - Nature Communications
Perez, Kimoto, Rajakumar and colleagues present a fast and accurate DNA sequencing method that reads canonical and non-canonical bases using AI and nanopore technology. The approach enables an expande...
nature.com
August 22, 2025 at 9:32 AM
Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com!
Read all about it here: nature.com/articles/s41...
Great collab with Chew and Hirao lab
x.com/NiranjanTW/s...
Read all about it here: nature.com/articles/s41...
Great collab with Chew and Hirao lab
x.com/NiranjanTW/s...
Reposted by Morten Kam Dahl Dueholm
#News&Views
Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.
#MicroSky
www.nature.com/articles/s41...
Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.
#MicroSky
www.nature.com/articles/s41...
Amyloids in bacterial antiphage defence - Nature Microbiology
Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.
www.nature.com
August 21, 2025 at 5:47 PM
#News&Views
Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.
#MicroSky
www.nature.com/articles/s41...
Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.
#MicroSky
www.nature.com/articles/s41...