Morten Kam Dahl Dueholm

Nice work. Did you by any chance look into the expression of the Fap functional amyloids (PA14_09300). It would be interesting to know if those are expressed and if so how it ranks among the transcripts. 😁

Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social

www.nature.com/articles/s41...

As a final note, I want to highlight that this approach is not restricted to #rRNA genes, but can be used for any amplicons used for microbial and #eDNA profiling! 🦠🧫🧬🪱🐛🐸🐟
#microsky #microbiomesky #protistsonsky

Finally, we show that the sequencing platform does not bias ASV relative abundances across environments, and that alpha-diversity measures are directly comparable!

Using increasingly complex communities, we demonstrate that the approach is broadly applicable to microbial communities.

Using the ZymoBIOMICS mock community, we show that we can recover perfect ASVs for essentially all theoretical ASVs ranging in size from 250 bp (V4) to 4200 bp (rRNA operons).

A new era for #ONT amplicon sequencing?
We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...

Type IV secretion systems: reconciling diversity through a unified nomenclature This review presents a comprehensive overview of Type IV Secretion Systems (T4SSs), focusing on their structural, functional, and evolutionary diversity ac

Happy to share a new review proposing a unified nomenclature for T4SSs.
Great collaboration with Peter J Christie, Gabriel Waksman, Ronnie Per-Arne Berntsson and our team.
academic.oup.com/femsre/artic...
#T4SS#Microbiology

The house that Kocuria built: A potential role for functional amyloid in the unique cube-based structure of K. varians biofilms Biofilm is the dominant growth mode of microorganisms, providing protection, surface adhesion and synergy between co-habiting organisms. Many aspects …

The house that Kocuria built: A potential role for functional amyloid in the unique cube-based structure of K. varians biofilms. 🦠🧫
www.sciencedirect.com/science/arti...

Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment - Microbiome Background Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized. Results In this study, w...

Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment
link.springer.com/article/10.1...

New 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.

Ktedonobacteria are so freaking cool, with 10+ Mbp genomes, interesting morphologies and tons of BGCs

Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence Abstract. Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which

Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence

#ISMEJournal from @alexrosado.bsky.social

academic.oup.com/ismej/advanc...

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

Announcing 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.

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github.com/bluenote-157...

The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta | PNAS Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant ag...

The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta

PNAS from @tlowepower.bsky.social

www.pnas.org/doi/10.1073/...

Friends don’t let friends publish in MDPI!

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...

New 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...

Constructing a “periodic table” of bacteria to map diversity in trait space Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

New 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...

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...

JB Editor's Choice: Ratnikava, Lamprecht & Sourjik explore the complex regulation of curli in Escherichia coli.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

My PhD student @andersohd.bsky.social made a very nice thread on what epsSMASH is and what it can do. bsky.app/profile/ande...

epsSMASH uncovers exopolysaccharide biosynthetic gene clusters in environmental and human microbiomes Biofilms represent the default mode of bacterial life in natural and built environments, with extracellular polysaccharides (exoPS) serving as essential structural and functional components of the bio...

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...

Sequencing Instrumrnt Outlook 2026

My observations & predictions on sequencing instrument companies

🧬🖥️

omicsomics.blogspot.com/2026/01/sequ...

Release Next time I'll try to be FASTA · tseemann/any2fasta New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

💾 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...

With all the excitement about AI giving us answers, we often forget that the real trick is to figure out what is the question.

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 🦠🧬🧫
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Useful discussion on circular contigs in metagenome assembly

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.

We anticipate that epsSMASH will become an essential tool for microbiologists who are interested in the EPS potential of their favorite species/community. We hope it's well received and welcome ideas for future versions!
8/8

epsSMASH is available as a user-friendly web-service with an interactive results page (a la antiSMASH) as well as a command-line tool for large-scale analysis of many genomes:

epsSMASH.org

github.com/AOHD/epsSMASH

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