@daanspeth
Computational microbiologist. Senior scientist at @cemess.bsky.social, @univie.ac.at. Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology. Maintainer of the GlobDB genome database https://globdb.org
We're pulling together the genomes for GlobDB release 232, which will be based on the upcoming GTDB release. We will also add new sources of genomes not in INSDC. Here's an overview of the data that will be included in the next GlobDB: globdb.org/news
Please contact me if we've missed something!🦠🖥️🧬
fair point, it should be a bit more intuitive now.
ah, the title is a link to the actual page... Sorry that wasn't clear
Today is the start of the 5th Analysing Microbial Genomic Data course at @unibirmingham.bsky.social #AMGDMar26 - in the last three years we’ve trained nearly 80 attendees from six countries and multiple UK universities
We're pulling together the genomes for GlobDB release 232, which will be based on the upcoming GTDB release. We will also add new sources of genomes not in INSDC. Here's an overview of the data that will be included in the next GlobDB: globdb.org/news
Please contact me if we've missed something!🦠🖥️🧬
Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳
mrc.tal.net/vx/mobile-0/...
A six panel comic of a man and a woman where their word balloons are actually other panels (there are no words) indicating future actions and explaining why they did what they did.
a three panel comic about Søren Kierkegaard in which the text of the man reads backwards and the dog forwards "Life can only be understood backwards" and the dog "but it must be lived forwards"
It's that time in my Making comics intro course when I talk image-text relations, which gives me an excuse to share 2 favorite comics that do bewildering things that can only be done in comics! Ibn Al-Rabin's seminal Le Verbe Prophétique alongside the always brilliant @tomgauld.bsky.social. So good!
We are currently recruiting PhD students, postdocs, and a group leader to join the Institute.
If you’re interested, please send me a personal message or email your CV and a brief motivation letter to: johannes.rebelein@hhu.de.
🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉
How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...
In the standard SEM image, aggregates of bacterial cells with no visible matrix sit on top of a network of collagen fibrils. In the cryo image, interconnected aggregates are covered with a smooth coat of matrix, and no collagen is visible - it is under the aggregates, and the only tissue structures visible are patches of elastin fibres.
If you check out my lab's recent work, you'll notice how much biofilm structure is destroyed by dehydration & vacuum during standard scanning electron microscopy. These are both images of P. aeruginosa PA14 #biofilm on pig lung tissue at 48h p.i: using cryoSEM retains the biofilm matrix. #MicroSky
Pacific Ocean Floor by MARIE THARP, Bruce Heezan, and Heinrich Berann, *as published in* the National Geographic. There, fixed it.😉
Remember! Applied and Environmental Microbiology solicits minireviews. And they are free to publish!
There's 2 more I want to write. Time in my career to summarize and rant.
🦠 Microbial friends - what is the BEST thing you've ever seen done in a teaching seminar demonstration during an interview? Pitch was to do an upper level micro lesson. Appreciate any tips for @micromal.bsky.social to consider.
Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.
We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵
With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268
This work is done together with talented MSc student Marcel Rennig. We intend to improve and expand on AASTK, so would welcome your feedback!
7/
AASTK can be installed from bioconda (conda install -c bioconda aastk), and is in active development on github (github.com/dspeth/aastk). Full documentation is available on the GlobDB website (globdb.org/aastk)
6/
Finally, Meta can be used to retrieve metadata for a set of protein sequences. Available metadata includes annotation, taxonomy, culture availability, and environmental association.
5/
Example CUGO plot. See AASTK documentation (https://globdb.org/aastk) for details
CUGO (colocated unidirectional gene organization) can be used to investigate and visualize consensus genomic context of protein sequences in a dataset. The CUGO plots can capture consensus genomic context of tens of thousands of sequences in one go.
4/
Example PASR plot. See AASTK documentation (https://globdb.org/aastk) for details
PASR (Protein alignment score ratio) can be used to find sequences of interest in a dataset, or create a reference database of a protein of interest.
3/
Example CASM plot. See AASTK documentation (https://globdb.org/aastk) for details
CASM (clustering alignment score matrix) is a tool designed to find structure in large protein datasets (eg >100k sequences of a complex superfamily). It can be used to cluster such datasets, visualize them in 2D, and annotate with available metadata (see below).
2/
Interested in microbial proteins and their diversity? 🖥️🧬🦠
We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences.
AASTK currently consists of 4 tools:
- CASM
- PASR
- CUGO
- Meta
1/
Long in the making, great to see the study on line at @femsmicro.org A novel North Sea ammonia-oxidizing archaeon Nitrosarchaeum marinum leverages a high abundance of transport systems to grow over a wide salinity range. #microbiology @ribesresearch.bsky.social academic.oup.com/femsec/artic...
Can't wait to release a 10-year-old birthday version for SeqKit!
- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads
Thank you all, dear contributors and users!
I'll keep maintaining it.
github.com/shenwei356/s...
The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.
Our new preprint introduces #kineochelins, a new group of #siderophores produced by the Antarctic soil actinomycete 🦠🔬🧫 #Actinokineospora sp. UV203
Kudos to the amazing Stanislava Králová & a fantastic team of collaborators 🤩
#microbiomesky
www.biorxiv.org/content/10.6...
Happy 38th birthday to the #LTEE!
#BOTD in 1988.
Keep on evolving!
#science #evolution #microbiology
Alita Burmeister (@aburmeister.bsky.social) is looking to hire a postdoc (or potentially a PhD student) for projects on phage resistance and evolution. The position description is posted to the Eco-Evo Jobs wiki and also available on her lab's website (arburmeister.weebly.com).
Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard!
With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution.
Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado
www.biorxiv.org/content/10.6...
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
