Daan Speth

The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology

Please share!

PhD position at the University of Copenhagen. Start date: 1st of June!
 
The project integrates field work, RNAseq, MALDI-MSI & FISH to explore composition, regulation, and resilience of termite host-gut symbiont metabolism.
 
👉 employment.ku.dk/phd?show=156...
 
⏳ Deadline 23/2/26

Bluesky Map Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

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

Postdoc in Archaea Microbiology - Vacancy at Aarhus University Vacancy at Department of Biology - Microbiology, Aarhus University

Postdoc position on Asgard archaea in Thiago’s new lab for someone well trained in biochemistry, cloning, and protein purification:
international.au.dk/about/profil...

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?

Then come and join our group !

How does catalysis emerge from non-catalytic domains?

In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.

A striking case of catalysis evolving from binding.

If they're the GTDB "species reps" then that numerical species name is a placeholder, but when publishing on them you could assign a name to the species using the SeqCode (registry.seqco.de).

The SeqCode considers a genome enough to validly name a species (and I agree). So I'd go with "unnamed"

The case that @uncultured.carinilab.com describes seems to be referring to genomes that can be classified to a genus by GTDBtk, but isn’t within 95% ANI of a GTDB genome.
For that case i agree genus sp. is most appropriate

are you asking about genomes that can be classified to the species level (ie within 95% ANI of a GTDB genome?). Then i would use the full numerical identifier to indicate that, and refer to them as “unnamed species”.

The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis Abstract. Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fun

New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...

Research Group Leader Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...

We are hiring for group leaders again — EBI is a great place to start your research group!

embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

And the plan is to update the resource following each new GTDB release, so the next release should come in May or so 🧬🖥️

if anything doesn't work I'd be very happy to hear about it, so I can make sure it does afterwards 👍

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

Essentially. There's a convenient overview figure in the (very short) paper: doi.org/10.1093/bioa...

There's a singleM metapackage available for download, as well as a sylph database. The taxonomy is consistent with, and an extension of, the GTDB taxonomy.

We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...

<i>Microbiology</i> Editors: Call for expressions of interest

Microbiology is seeking Editors to help ensure the publication of high-quality research and to foster engagement across the microbiology community.
Expertise in biotechnology, regulation, sensing, signalling or AMR is especially welcome.
🗓️ Apply by 16 February: https://microb.io/4qKdgJ6

🦠🖥️🧬

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

(1/10)

for reads under 1kb straight up diamond blastx might work, but then you're of course doing a two stage analysis and might be overengineering it (depending on Q).

Also going to briefly (and selfishly) mention the GlobDB here again, because I want it stuck in the heads of the vocal folks on here 😅

the GlobDB (globdb.org) is the better option here. Full taxonomy but twice as many species reps as the GTDB. Those extra 50% are also biased towards less characterized environments because those big metagenome studies don't end up in INSDC dbs anymore (and thus fo missing from GTDB).

i would use either singleM or sylph with the GlobDB databases available for them from globdb.org. Double the number of species reps relative to GTDB.

Also would genuinely be interested to see the comparison of both profilers

Uppsala in late autumn

Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Full Professor and Chair Laboratory of Biophysics We are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR)

www.wur.nl/en/vacancy/f...

Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!

We have two funded postdoctoral positions available. Topics encompass:

-Next gen light-sheet fluorescence microscopy instrumentation

-Structured illumination microscopy and other approaches to extend the resolution limit.

-Nonlinear microscopy combined with adaptive optics / phase conjugation

What were the first animals? The fierce sponge–jelly battle that just won’t end For almost two decades, scientists have debated whether sponges or comb jellies are the first animal lineage. Now some are calling for a more harmonious approach.

On the importance of preprints, regardless of whether you are Team Sponge or Team Jelly:

'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'

www.nature.com/articles/d41...

Here’s my 3-step framework to learn Bioinformatics or learn anything in life 👇

With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.

More info:
globdb.org/news

Thanks #anvio team!
🖥️🧬🦠

Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)