Come study carbodioxyphiles with us as part of ERC Archean Park! Deadline approaching soon so feel free to reach out and please share the opportunity with your networks!! 🌋

The Probst Lab@probstlab.bsky.social · last mo.

Not too long left to apply to this great position here in Essen with us! Come work on ERC project Archean Park and uncover carbodioxyphilic metabolisms around the world! 🌋🧬🥼💻

Come work with us, we're really cool people to hang out with 😁 You'll get to do interdisciplinary research exploring microbial metabolisms during the Archean Eon by investigating the deep biosphere in high-CO₂ ecosystems hundreds of meters below ground. Please retweet and spread the word! 🧬 💻

The Probst Lab@probstlab.bsky.social · 2mo ago

We're looking for a Postdoctoral Researcher (f/m/d) for the ERC Synergy project “Archean Park”! 📍 Location: Essen, Germany ⏱ Duration: 36 months (Full-time | EG 13 TV-L) 📅 Start Date: As soon as possible ⏰ Application Deadline: September 2, 2026 www.uni-due.de/karriere/ste...

Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

go.nature.com

Endosymbionts inside #mitochondria that themselves started as #endosymbionts? Uncovering the biological Matryoshka doll, membrane by membrane, using volume electron microscopy. #microbiology #endosymbiosis #symbionts #MicroSky www.nature.com/articles/s42...

🤯 Manual MAG refinement? Still doing it by hand?? We’ve been there... You could just leave those messy, ill-assigned contigs/scaffolds in your data for NCBI to pick up during your submission… …OR you could add itBins, our new automated MAG refiner by @jmk-ude.bsky.social, to your pipeline!! 🔥

New version of OrfM, a simple and not slow open reading frame (ORF) caller, is out. Still simple, but a port from C to Rust gained ~25% on runtime. Now with an API too. github.com/wwood/OrfM

GitHub - wwood/OrfM: simple and not slow ORF caller

simple and not slow ORF caller. Contribute to wwood/OrfM development by creating an account on GitHub.

github.com

I mean look at this baby! Right out from 115m depth! 🔥🔥

We’re out and about yet again, this time in the vulcanic Eifel region drilling with Jens Kallmeyer @gfz.bsky.social 🌋

"Working in academia can be stressful. Laurel Raffington suggests treating it as ‘just a job’ to reduce performance pressure and advocate for structural improvements." "Academia is just a job" by @laraffington.bsky.social (2025, Nature Human Behavior) www.nature.com/articles/s41...

Academia is just a job - Nature Human Behaviour

Working in academia can be stressful. Laurel Raffington suggests treating it as ‘just a job’ to reduce performance pressure and advocate for structural improvements.

nature.com

Near-zero temperatures, but field sampling is still a-go for the Probst lab 😎 @geomicrosoares.bsky.social @feriel.bsky.social @pengyaoz.bsky.social are out in Regensburg! @unidue.bsky.social @uniregensburg.bsky.social

Hi #bioinformatics folk, I want to quickly extract metagenome reads that map to medium-sized piles of reference genomes (100s-1000s, but not 10_000s). I don't _necessarily_ care about the exact position. I'm using minimap2 right now but it's kinda choking on 1000 microbial genomes at once. Thoughts?

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file. No RNA-seq. No protein homology. No repeats, hints, or curated evidence. Raw genome → accurate gene models. Deep learning + HMM, published in @natmethods.nature.com www.nature.com/articles/s41...

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods

By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

nature.com

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing

A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

github.com

A geothermal amoeba sets a new upper temperature limit for eukaryotes https://www.biorxiv.org/content/10.1101/2025.11.24.690213v1

@katharinasures.bsky.social @probstlab.bsky.social et al. analysed CRISPR-Cas systems of metagenome-assembled genomes from two subsurface environments, shedding new light on the diversity of CRISPR spacers in natural microbial communities. 🔗 doi.org/10.1093/gbe/evaf201 #genome #evolution #CRISPR

Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments

Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

doi.org

ICYMI: New online! Microbial genomics for antimicrobial resistance ecology and action

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...

Metalog: curated and harmonised contextual data for global metagenomics samples

Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

academic.oup.com

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research

Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

academic.oup.com

Still using 16S/ITS profiling? You might want to reconsider👀 Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable! microbiomejournal.biomedcentral.com/articles/10....

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome

Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

microbiomejournal.biomedcentral.com

Microbial Considerations for the Permanent Geological Storage of CO2 enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Microbial Considerations for the Permanent Geological Storage of CO2

The impacts of microbiology on the storage of CO2 are poorly understood but could be critical to its safe geological disposal. We review evidence for microbial risks and opportunities, and argue for ...

enviromicro-journals.onlinelibrary.wiley.com

In the meantime, we've been collecting a list of these at tinyurl.com/mag-collecti.... Feel free to add more you find. See also GlobDB from @daanspeth.bsky.social which incorporates some of these into a new MAG collection arxiv.org/abs/2506.11896

Public MAG datasets not available at NCBI or ENA

Some metagenome assembled genome (MAG) datasets are not available in the standard locations (NCBI / ENA / etc) for a variety of reasons. Here you can contribute new ones you come across. To be recorde...

tinyurl.com

Evidence from 14 research funding programmes confirms that early winners tend to keep winning (Matthew effect). But the idea that an early setback makes you stronger later doesn’t replicate widely. buff.ly/UEtcRd4

Please share this with anyone who may be interested in a post-doc in Germany: jobs.awi.de/Vacancies/20... This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.

Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov Free access link: rdcu.be/eLtCH 🧵 by @yifanzhou.bsky.social 👇

Yifan ZHOU@yifanzhou.bsky.social · 12mo ago

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...

Are you, or someone you know, looking for a PhD, starting in Oct 2026? Do you like bacteria, genomics & puzzles?🦠🧬🧩 Do you wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social? Please apply or share by 2 Dec 🗓️ #PhDposition #academicsky Find out more ⬇️

"Want to start using Nanopore technology to research protistan diversity? Check out our paper introducing a pipeline for creating OTUs from Nanopore metabarcodes — bridging the gap between short- and long-read metabarcoding." - Anna Karnkowska doi.org/10.3897/mbmg...

To celebrate and support the great @blackinmicro.bsky.social initiative and what joining could mean for you, please take a look through the commentary in Microbial Genomics @microbiologysociety.org hot off the press today! #MicroSky #MicrobiomeSky 💻🧬🧪🦠 www.microbiologyresearch.org/content/jour...

Reclaiming microbiology: scientists as community members and advocacy leaders

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefi...

microbiologyresearch.org

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro@robp.bsky.social · 12mo ago

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Staff Scientist

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

embl.wd103.myworkdayjobs.com