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
Respiratory 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...
Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!
doi.org/10.1093/isme...
Validate User
doi.org
December 5, 2025 at 4:20 PM
Respiratory 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...
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...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 5, 2025 at 11:03 AM
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
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...
academic.oup.com/ismecommun/a...
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome
Abstract. Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in waste
academic.oup.com
December 5, 2025 at 10:49 AM
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...
academic.oup.com/ismecommun/a...
Reposted by Morten Kam Dahl Dueholm
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/12/04/d...
• urinary biochem ecology / @mikeneugent.bsky.social
• Microflora Danica atlas / @mkddueholm.bsky.social
• gut lumen -> hypothalamus / @pipethero.bsky.social
See you next week at #MVIF 44 (@microbiomevif.bsky.social)!
• urinary biochem ecology / @mikeneugent.bsky.social
• Microflora Danica atlas / @mkddueholm.bsky.social
• gut lumen -> hypothalamus / @pipethero.bsky.social
See you next week at #MVIF 44 (@microbiomevif.bsky.social)!
December 05, 2025
See you at MVIF next week! General microbiome Consensus Statement: STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies – Julia M. Kelliher …
microbiomedigest.com
December 5, 2025 at 6:11 AM
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/12/04/d...
• urinary biochem ecology / @mikeneugent.bsky.social
• Microflora Danica atlas / @mkddueholm.bsky.social
• gut lumen -> hypothalamus / @pipethero.bsky.social
See you next week at #MVIF 44 (@microbiomevif.bsky.social)!
• urinary biochem ecology / @mikeneugent.bsky.social
• Microflora Danica atlas / @mkddueholm.bsky.social
• gut lumen -> hypothalamus / @pipethero.bsky.social
See you next week at #MVIF 44 (@microbiomevif.bsky.social)!
Reposted by Morten Kam Dahl Dueholm
Excited 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...
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...
December 3, 2025 at 4:00 PM
Excited 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...
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...
Reposted by Morten Kam Dahl Dueholm
#Resource
HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.
#MicroSky #MicrobiomeSky 🦠💻
www.nature.com/articles/s41...
HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.
#MicroSky #MicrobiomeSky 🦠💻
www.nature.com/articles/s41...
A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models - Nature Microbiology
HRGM2 is a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut micro...
www.nature.com
December 4, 2025 at 3:27 PM
#Resource
HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.
#MicroSky #MicrobiomeSky 🦠💻
www.nature.com/articles/s41...
HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.
#MicroSky #MicrobiomeSky 🦠💻
www.nature.com/articles/s41...
Reposted by Morten Kam Dahl Dueholm
Forskere fra Aalborg Universitet har navngivet over 1.000 hidtil ukendte mikroorganismer, fundet i dansk jord, efter danske byer som Hadersleviella, Glyngoereum og Rungstediana. Projektet Microflora Danica kortlægger Danmarks mikrobielle diversitet.
Flere danske byer har fået en mikroorganisme opkaldt efter sig
På Aalborg Universitet har forskere kortlagt arvematerialet på mere end 15.000 hidtil ukendte mikroorganismer og bakterier.
www.dr.dk
September 9, 2025 at 12:16 PM
Forskere fra Aalborg Universitet har navngivet over 1.000 hidtil ukendte mikroorganismer, fundet i dansk jord, efter danske byer som Hadersleviella, Glyngoereum og Rungstediana. Projektet Microflora Danica kortlægger Danmarks mikrobielle diversitet.
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...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 3, 2025 at 8:50 PM
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...
www.nature.com/articles/s41...
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...