Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms
bioRxiv by Gabriel Antonio S. Minero et al
with @thethormannden.bsky.social, Rikke Louise Meyer
www.biorxiv.org/content/10.6...
And the poster is up at #microbio26! Come and find me at A037 to talk all things biofilm :)
@microbiologysociety.org
Want to annotate a bacterial genome with structures?
@oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures
www.biorxiv.org/content/10.6...
#phagesky #microsky #microbiomesky
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
I was reminded of this paper from colleagues at AAU:
"We ... miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities."
journals.plos.org/plosone/arti...
Want to convert old relative abundance ocean amplicon data into absolute abundances? Williams et al. show a flow cytometry "anchor" can provide reasonable absolute abundances, validated by internal-standard corrected metagenomics with single copy genes, and amplicons academic.oup.com/ismecommun/a...
On the architecture and evolution of prokaryotic multicellularity
Preprint from @escolizzi.bsky.social
www.authorea.com/doi/full/10....
Moore, Gitai and colleagues report "CauloKO:an ordered transposon mutant library in Caulobacter crescentus", and use my favorite assay - a crystal violet screen for biofilm mutants, validating the libray and identifying new mutants.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
Are you still adding to this? I would like a spot 🙏
Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows.
We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠
Here's what we found 👇
doi.org/10.1128/msystems.01062-25
If we're going to solve this we need to have an honest and informed conversation about the true costs of doing things 2/2 journals.plos.org/plosbiology/...
Framework for microbiome-inspired functional synthetic communities
One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...
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 www.biorxiv.org/content/10.64898/2026.02...
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.
