Anders Ogechi Hostrup Daugberg

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...

Spatial structure: shaping the ecology and evolution of microbial communities Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

A national baseline for methane sink habitats and methanotroph diversity https://www.biorxiv.org/content/10.64898/2026.02.02.703227v1

More microbiologists need to think about goop! We only found 31 studies to compare our results to, mostly clinical gammaproteobacteria.

Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/

Sounds cool! Thanks for the share!

Pel is in there! It's a crazy widespread operon.
I checked the reference genome for R. solanacearum (Str. IBSBF1503) and pel is in there as well (but no PNAG)

epssmash.secondarymetabolites.org/upload/bacte...

Running the ASM225169v1 assembly, epsSMASH finds four exoPS clusters in K60! The "putative_wzy_dependent" is EPS-I, the other putative might be the ops cluster! The well-known pel and PNAG operons are also found in K60, but they don't seem to have been described much in literature.

Such a cool exopolysaccharide, and a really fascinating story!

Also happy to report that epsSMASH detects the Ralstonia EPS-I gene cluster 🙌

🧫🦠🧬🖥

YouTube video by American Society for Microbiology Bioflim Formation and the Dust Microbiome

Dust looks dead but it is, in fact, alive, teeming with hardy microbes traveling around the world. How are they surviving the trip? Scientists think biofilm formation may play a role. Watch Microbial Minutes for the full story! 🦠 youtu.be/3q-rhw17h2o

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...

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.

#MicrobiomeSky
#MicroSky
#GeneSky

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

7/8

Novel systems:
We investigated the largest uncharacterised GCF from activated sludge BGCs, revealing it to be a novel exoPS system conserved in almost every genera in the order Sphingomonadales. Analysis of the genes in the BGC suggests that it is involved in the PEP-CTERM/exosortase system!
6/8

Distant homologs: epsSMASH detected BGCs containing the core machinery for Pel biosynthesis in several phyla where Pel operons had not been detected before. Using structural homology searches we confirmed that these BGCs were indeed distant homologs of the canonical Pel operon!
5/8

To explore this vast expanse of exoPS "dark matter", we built gene cluster families (GCFs) of all detected exoPS BGCs. Known and uncharacterised BGCs grouped into distinct, phylogenetically conserved GCFs. These GCFs represented distant homologs of known systems as well as completely novel ones.
4/8

We ran epsSMASH on four HQ genome catalogues, representing microbiomed from the human gut, soil, ocean and activated sludge, detecting a median of 1-2 BGCs/genome. Strikingly, most (62-96%) of the BGCs in all four biomes were found by our "loose" rules and had never been characterised before.
3/8

epsSMASH workflow and workflow for creating epsSMASH rules.

epsSMASH uses custom pHMMs and manually curated rules to detect BGCs across all four types of exoPS biosynthesis (Synthase, Wzx/Wzy, ABC transporter and Sucrase-dependent). Rulesets with different strictness allows for the detection of known exoPS BGCs, distant homologs and novel systems.
2/8

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

⭐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

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…

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...

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...

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!

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

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.

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...

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...

#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...

The abstract submission link is hidden a bit on the website, but if all else fails ctrl+f "Abstract registration" should fetch it.