Anders Ogechi Hostrup Daugberg
@andersohd.bsky.social
PhD fellow at Aalborg University 🇩🇰
Using 'omics to study bacteria which secrete biopolymers (the backbone of biofilms!) 🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA 🧬
Using 'omics to study bacteria which secrete biopolymers (the backbone of biofilms!) 🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA 🧬
Pinned
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
Reposted by Anders Ogechi Hostrup Daugberg
Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
December 26, 2025 at 3:38 PM
Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
December 24, 2025 at 12:48 PM
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
Reposted by Anders Ogechi Hostrup Daugberg
⭐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
🧬 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
December 22, 2025 at 3:48 PM
⭐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
🧬 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
Reposted by Anders Ogechi Hostrup Daugberg
Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...
gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota
Microbiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta…
www.sciencedirect.com
December 13, 2025 at 7:41 AM
Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...
Reposted by Anders Ogechi Hostrup Daugberg
New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species.
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
December 10, 2025 at 12:43 PM
New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species.
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Another fruitful collaboration with the Otzen group 🦠🧫🧬
We looked for curli and Fap operons across the bacterial tree of life (GTDB v226), and found that while Fap operon synteny and FapC repeat numbers are remarkably conserved, the opposite is true for curli operons and csgA!
We looked for curli and Fap operons across the bacterial tree of life (GTDB v226), and found that while Fap operon synteny and FapC repeat numbers are remarkably conserved, the opposite is true for curli operons and csgA!
December 7, 2025 at 9:17 AM
Another fruitful collaboration with the Otzen group 🦠🧫🧬
We looked for curli and Fap operons across the bacterial tree of life (GTDB v226), and found that while Fap operon synteny and FapC repeat numbers are remarkably conserved, the opposite is true for curli operons and csgA!
We looked for curli and Fap operons across the bacterial tree of life (GTDB v226), and found that while Fap operon synteny and FapC repeat numbers are remarkably conserved, the opposite is true for curli operons and csgA!
Reposted by Anders Ogechi Hostrup Daugberg
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
Reposted by Anders Ogechi Hostrup Daugberg
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 Anders Ogechi Hostrup Daugberg
#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...
Via the REThiNk project we are organising a conference on Environmental biofilms and flocs: matrix composition, properties and applications" at the beautiful waterfront in Aalborg, Denmark in April 2026 🦠🧫🧬
Abstract submission is open, check out the link below!
www.eps26.bio.aau.dk
Abstract submission is open, check out the link below!
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 12:30 PM
Via the REThiNk project we are organising a conference on Environmental biofilms and flocs: matrix composition, properties and applications" at the beautiful waterfront in Aalborg, Denmark in April 2026 🦠🧫🧬
Abstract submission is open, check out the link below!
www.eps26.bio.aau.dk
Abstract submission is open, check out the link below!
www.eps26.bio.aau.dk
Reposted by Anders Ogechi Hostrup Daugberg
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 Anders Ogechi Hostrup Daugberg
Let me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪:
pmc.ncbi.nlm.nih.gov/articles/PMC...
You can read our news and views here: www.pnas.org/doi/10.1073/...
pmc.ncbi.nlm.nih.gov/articles/PMC...
You can read our news and views here: www.pnas.org/doi/10.1073/...
November 13, 2025 at 4:13 PM
Let me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪:
pmc.ncbi.nlm.nih.gov/articles/PMC...
You can read our news and views here: www.pnas.org/doi/10.1073/...
pmc.ncbi.nlm.nih.gov/articles/PMC...
You can read our news and views here: www.pnas.org/doi/10.1073/...
Reposted by Anders Ogechi Hostrup Daugberg
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Reposted by Anders Ogechi Hostrup Daugberg
Opinion: Chaos is coming for scholarly publishing.
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Chaos is coming for scholarly publishing - Research Professional News
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards
www.researchprofessionalnews.com
November 12, 2025 at 10:17 AM
Opinion: Chaos is coming for scholarly publishing.
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Reposted by Anders Ogechi Hostrup Daugberg
DMS 2025 is a wrap! 🧫
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
November 11, 2025 at 10:59 PM
DMS 2025 is a wrap! 🧫
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
Reposted by Anders Ogechi Hostrup Daugberg
1/ Working with big data in R?
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
November 11, 2025 at 2:45 PM
1/ Working with big data in R?
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Reposted by Anders Ogechi Hostrup Daugberg
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
November 4, 2025 at 2:42 PM
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
Reposted by Anders Ogechi Hostrup Daugberg
Cellulose biosynthesis and function in Streptomyces
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
Cellulose biosynthesis and function in Streptomyces
Cellulose, a ubiquitous polysaccharide with critical roles in life, provides structural
integrity to cells in plants and aids biofilm formation in many bacteria. Although
bacterial cellulose biosynthe...
www.cell.com
October 30, 2025 at 12:50 PM
Cellulose biosynthesis and function in Streptomyces
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
Reposted by Anders Ogechi Hostrup Daugberg
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 Anders Ogechi Hostrup Daugberg
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 24, 2025 at 9:15 AM
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Anders Ogechi Hostrup Daugberg
Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
October 15, 2025 at 8:01 AM
Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
Reposted by Anders Ogechi Hostrup Daugberg
PhD opportunity in my lab: exploring how commensals and pathogens build biofilm communities on endotracheal (ventilator) tubes. Microbial ecology, medical microbiology and fancy imaging! Co-supervised with the fabulous Saskia Bakker and Jeremy Webb warwick.ac.uk/fac/cross_fa... #MicroSky
Dr Freya Harrison
Dr Freya Harrison
warwick.ac.uk
October 15, 2025 at 8:09 PM
PhD opportunity in my lab: exploring how commensals and pathogens build biofilm communities on endotracheal (ventilator) tubes. Microbial ecology, medical microbiology and fancy imaging! Co-supervised with the fabulous Saskia Bakker and Jeremy Webb warwick.ac.uk/fac/cross_fa... #MicroSky
Reposted by Anders Ogechi Hostrup Daugberg
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
Staphylococcus aureus infections represent a clinical challenge due to their propensity to form biofilms and the increasing prevalence of antibiotic r…
www.sciencedirect.com
September 19, 2025 at 11:23 AM
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
Reposted by Anders Ogechi Hostrup Daugberg
Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.
September 5, 2025 at 3:20 PM
Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.