www.gfz.de/en/career/jo...
4-year PhD position in Geomicrobiology in our #ERCSyg project Archean Park. Come work with us at @gfz.bsky.social and collaborate with @probstlab.bsky.social, @marumunibremen.bsky.social, @uni-muenster.de. Flexible starting date, Application until May 3.

👉 Read the preprint, led by @jmk-ude.bsky.social: www.biorxiv.org/content/10.6...

Let us know what you think, and leave no MAG unrefined!

github.com/ProbstLab/it...
🐍 $ mamba install bioconda::itbins

@geomicrosoares.bsky.social @alexjprobst.bsky.social @unidue.bsky.social @unimarburg.bsky.social

Figure 1 shows the conceptual workflow of the algorithm. It first loads the configuration file and the input data of one or multiple binned metagenomes, yet evaluates each bin individually. It then iteratively processes each candidate bin in the input, going through the refinement tasks, potentially multiple times. The refinement either stops when the last step or a preset stop task have been reached or an unrecoverable error has been encountered. The algorithm tasks can be configured individually.

🤯 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!! 🔥

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

@alexjprobst.bsky.social look at this, we’re drilling over here!! 🥳

@unidue.bsky.social @erc.europa.eu

@geomicrosoares.bsky.social @katharinasures.bsky.social @feriel.bsky.social @pengyaoz.bsky.social

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

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

Sorry Alex we meant @alexjprobst.bsky.social not you :)

We analysed more than 1 TB of sequencing data and discovered that CRISPR-Cas systems in two subsurface environments acquire spacers matching multiple prokaryotes in the same environment.

This provides an explanation for some of the many unmatched spacers in public databases.

@unidue.bsky.social

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

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬

Have a read!! ➡️ doi.org/10.1093/gbe/...

@emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!

They made up the Data Reuse Core Team along with @lhug.bsky.social @environmicrobio.bsky.social @folker.bsky.social and had the support of the Data Reuse Consortium, composed of 167 scientists globally who were pivotal in driving this effort forward! Thank you all! 🧬

@unidue.bsky.social

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our own @alexjprobst.bsky.social @geomicrosoares.bsky.social and Cristina Moraru have recently authored a @natmicrobiol.nature.com Consensus Statement where they discuss new mechanisms for sequencing data reuse! 🧬💻

Check out their manuscript here:
www.nature.com/articles/s41...

@alexjprobst.bsky.social @geomicrosoares.bsky.social & Till Bornemann from our group were part of this effort!

Shoutout to the remainder collaborators at the China University of Geosciences, and Jon Lloyd at the University of Manchester (@manchesterup.bsky.social).

@unidue.bsky.social & others RT!

We tracked nucleotide diversity in MAGs across different mining stages, which suggested widespread mutational pressure under long-term environmental stress!

We leveraged #metagenomics & #metatranscriptomics data to estimate microdiversity in groundwater at different stages of U mining.

We show that U in-situ leaching drives significant alterations in 🦠 community composition, oxidative stress, biogeochemical cycling, and overexpression of 🧬 repair genes

Uranium mining fuels evolution in deep groundwater microbiomes Microbial communities in the deep biosphere underpin global biogeochemical cycles, yet their evolutionary responses to extensive anthropogenic disturbances remain unclear. Uranium in-situ leaching (IS...

Fresh out of the oven! 🍞
We're happy to see this preprint out, fruit of a recent collaboration with @wei-biogeochem.bsky.social! 🧬💻

Small 🧵 below going through the main points 👇
www.biorxiv.org/content/10.1...

Please RT this awesome opportunity to do a PhD at @unidue.bsky.social in collaboration with @jgi.doe.gov!! 🔥 Thanks!

We’re happy to announce Dr. Lennard Stach!! 🥳🥳 Well done Lennard for a brilliant defense and thesis!! We will miss you!
Finally, thank you @leeselab.bsky.social for sitting in the thesis committee! 🫶

Our @umweltstiftung.bsky.social fellow Linda Labecka presented her work at the most recent DBU conference! She works closely with the Institute for Artificial Intelligence in Medicine (@unidue.bsky.social & University Medicine Essen) and Universitätsklinikum Bonn (@unibonn.bsky.social)! 🧬💻

Differential Expression of Core Metabolic Functions in Candidatus Altiarchaeum Inhabiting Distinct Subsurface Ecosystems Major differences between Candidatus Altiarchaeum species living in two distinct subsurface ecosystems as determined via metatranscriptomics. Genes overly expressed in different Ca. Altiarchaea in Mu...

Our latest work is out - here, our own Dr. Sarah Eßer compares transcriptomic patterns of Altiarchaeum in Crystal Geyser (US) and the Muehlbacher sufidic spring (Germany)! 🧬
Read more below:
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

a person in a lab coat with the word let 's do this ALT: a person in a lab coat with the word let 's do this

Excited to welcome @hsintunglai.bsky.social and @renaandraes.bsky.social as PhD students to our group!! They will be working within Phase 2 of @crc-resist.bsky.social @unidue.bsky.social under the supervision of @alexjprobst.bsky.social and @cristinamoraru.bsky.social.

#TBT to @joernstarke.bsky.social and @katharinasures.bsky.social presenting their amazing work at the @vaam-microbes.bsky.social AC 2025 which took place at @ruhr-uni-bochum.de just last week! Well done you two!
@crc-resist.bsky.social @unidue.bsky.social

Here's our latest group photo! Our lovely team keeps growing, as does our enthusiasm for doing great science together! 🦠🧬

Here’s @joernstarke.bsky.social !! 🥳

Then on Wednesday 9.30am at Lecture Hall 5, @katharinasures.bsky.social who recently started her PhD with us will tell us more “New insights into the spacer diversity of CRISPR-Cas systems in natural environments”, a collab with @emilruff.bsky.social ! 🧬💻

On Tuesday 12.30pm at Lecture Hall 7, our own Jörn Starke is presenting on “Flow Velocity and Anthropogenic Stressors Drive Microbial Community Dynamics in Riverine Ecosystems”, right out of @crc-resist.bsky.social and our role at @unidue.bsky.social in that project! 🏞️

We’re looking forward to meeting all our science friends at the @vaam-microbes.bsky.social Annual Conference 2025 at @ruhr-uni-bochum.de !! 🧬🦠

On our side, we’re exceptionally giving two talks about our latest work:
⬇️

Super happy to be hosting Prof. Richard Allen White III AKA @raw937.bsky.social from the University of North Carolina at Charlotte at @unidue.bsky.social for 3 surprisingly sunny weeks!! Great to have you around Rick!! 🦠🧬