@andersohd
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 🧬
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...
New preprint alert! We conducted a long-term evolution experiment to ask: How do species interactions shape adaptive evolution in microbial biofilms? #biofilm #LTEE
www.biorxiv.org/content/10.6...
1/5
Now out in @natcomms.nature.com :
versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities.
Read the full paper here #openaccess:
www.nature.com/articles/s41...
“Many of the planet’s microbiomes are under serious threat, with untold numbers of species & ecosystems flickering silently out of existence.”
— @moiradonovan.bsky.social
#microbes #microbiome #conservation #environment
🔖 kucharski AI and science research
Kids: “Dad that car cut you off!”
Me: “He’s harmless.”
This is a major issue is that the incentives are to output false positives in your tools
If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it!
open.substack.com/pub/luispedr...
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...
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 🙌
🧫🦠🧬🖥
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
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