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Alex Probst

@alexjprobst.bsky.social
1.4K followers 600 following 48 posts

Professor for Microbiology at Research Alliance Ruhr, Uni-DUE, #ERCSyg awardee, member of CRC RESIST #microbiome #omics #microscopy #ecophysiology Free time: Dad, weight training, cs2, nature, bbq, board games, pottery

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Reposted by Alex Probst
Ryo Harada @ryoharada.bsky.social · 09/10/2026
Finally, our Sukunaarchaeum paper is out in Current Biology!! authors.elsevier.com/c/1nvtC3QW8S...
cell.com
A hidden archaeal lineage with an ultra-reduced genome retaining only its replicative core
Harada et al. describe an archaeon, recovered from a single marine plankton cell, whose 238-kb genome is the smallest known for the domain. It has lost nearly all metabolism but keeps the machinery to...
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The Probst Lab @probstlab.bsky.social · 07/08/2026
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...
uni-due.de
Stellenausschreibung
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alepfu.bsky.social @alepfu.bsky.social · 26/05/2026
Want to profile microbial communities, but your reference database is weak? Take a look at SGenerator, our LSTM-based approach for generating full-length 16S rRNA sequences for underrepresented genera. doi.org/10.1093/isme... #Bioinformatics #MicrobialEcology #MachineLearning
Screenshot of the paper title, with journal and citation information.
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The Probst Lab @probstlab.bsky.social · 02/04/2026
🤯 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!! 🔥
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.
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The Probst Lab @probstlab.bsky.social · 07/03/2026
@alexjprobst.bsky.social look at this, we’re drilling over here!! 🥳
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Alex Probst @alexjprobst.bsky.social · 27/12/2025
I don’t trust the metaspades flag. The workflow Meren linked below would work to. If you need other/our scripts, email me
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Alex Probst @alexjprobst.bsky.social · 27/12/2025
either use anvio or send me an email and we can share our scripts to find circular contigs from sam files.
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Alex Probst @alexjprobst.bsky.social · 27/12/2025
Depends on the length of the contigs. for long contigs, you need to find paired reads where one of them maps at one end and the other at the other end. You should have multiple read pairs fulfilling that criterion. Yet, it’s way more complicated if the contigs are short!
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Alex Probst @alexjprobst.bsky.social · 17/11/2025
If you wanna take over my job for a few months, by all means 🤣🤣🤣
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Alex Probst @alexjprobst.bsky.social · 14/11/2025
indeed!!!!
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Reposted by Alex Probst
Laborjournal @laborjournal.bsky.social · 12/11/2025
Daten sind zum Teilen da: Alexander Probst von der Universität Duisburg-Essen und Kolleg:innen haben ein Konzept für die faire Nachnutzung öffentlicher Mikrobiom-Sequenzdaten entwickelt. Larissa Tetsch hat mehr dazu 👉 www.laborjournal.de/editorials/3... @alexjprobst.bsky.social @unidue.bsky.social
Links: Grafik einer DNA-Helix vor einem weiß/roten Binärcode. Rechts daneben steht die Überschrift des im Post verlinkten Artikels: „Daten mit Erkennungsmarke“. Es folgt dessen Vorspann mit dem Text: " In die Erhebung öffentlich zugänglicher Sequenzdaten ist oft viel Zeit und Geld geflossen. Das sollte besser gewürdigt werden, findet ein Konsortium aus der Mikrobiologie“…
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The Probst Lab @probstlab.bsky.social · 30/09/2025
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...
nature.com
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.
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Reposted by Alex Probst
Roland Hatzenpichler @environmicrobio.bsky.social · 26/09/2025
Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk
tinyurl.com
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.
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Alex Probst @alexjprobst.bsky.social · 26/09/2025
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com! Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
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Alex Probst @alexjprobst.bsky.social · 24/09/2025
Congrats, Ralf et al! :)
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Reposted by Alex Probst
Ecotoxicology lab RC One Health Ruhr @ecotox.bsky.social · 24/09/2025
Exciting collaboration with colleagues from the US and Frederik de Laender - lead by S. Rumschlag and Mike Mahon - on how climate change has lead to alterations in US fish diversity over the last decades. Paper just out: www.nature.com/articles/s41...
nature.com
Diverging fish biodiversity trends in cold and warm rivers and streams - Nature
In the past three decades, fish abundance, richness and uniqueness have diverged across cold and warm streams, and the effects on native fish communities of stream warming and increases in introduced fishes have magnified each other.
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Alex Probst @alexjprobst.bsky.social · 19/09/2025
it was a pleasure, Gary!
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Reposted by Alex Probst
Gareth (Gary) Trubl @gtrubl.bsky.social · 19/09/2025
New paper alert with @alexjprobst.bsky.social. enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication
The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...
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Alex Probst @alexjprobst.bsky.social · 01/09/2025
cool paper, congrats! have you considered naming it under the @seqcode.bsky.social instead of calling it a Candidatus which has no priority?
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Anne Daebeler @anne-daebeler.bsky.social · 01/09/2025
📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations. www.biorxiv.org/content/10.1... #microbesky #microbiomesky
biorxiv.org
Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland
Methanotrophic bacteria in peatlands mitigate emissions of methane (CH4), a potent greenhouse gas. Yet, the identity, physiology, and adaptive traits of methanotrophs inhabiting acidic peatlands are s...
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Alex Probst @alexjprobst.bsky.social · 29/08/2025
Mein Beileid, liebe Sigrid. Fühl dich gedrückt.
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Alex Probst @alexjprobst.bsky.social · 23/08/2025
I also got only one spot here… they are really rare unfortunately…
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Alex Probst @alexjprobst.bsky.social · 23/08/2025
did you buy them or „hunt“ them? ;)
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Alex Probst @alexjprobst.bsky.social · 22/08/2025
Congrats, Matt! Can‘t wait to see your latest results! Hopefully some new cool tools :)
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André Soares @geomicrosoares.bsky.social · 31/07/2025
The Central Collection of Algal Cultures (CCAC) at @unidue.bsky.social is advertising a 3-year PhD position supervised by the current Curator, Dr. Olga Matantseva! This PhD will take place in close collaboration with the @jgi.doe.gov. 🦠🧬💻 Apply here: www.uni-due.de/karriere/ste...
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Nature Microbiology @natmicrobiol.nature.com · 08/08/2025
#NatMicroPicks Hidden microbial world in trees🌳 Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function. #PlantMicro #MicroSky www.nature.com/articles/s41...
nature.com
A diverse and distinct microbiome inside living trees - Nature
Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...
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The Probst Lab @probstlab.bsky.social · 07/08/2025
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...
biorxiv.org
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...
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Alex Probst @alexjprobst.bsky.social · 07/08/2025
We once collaborated with another lab by analyzing metagenomes (create MAGs, analyze the metabol. etc). The PI asked me for a conversation during which he explained to me that the work we do is technical & no real contribution. He does not consider bioinformatics science. Never worked w/ him again.
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Alex Probst @alexjprobst.bsky.social · 07/08/2025
There exist some metrics that do not consider multi-author papers even though someone is corresponding/first/last author. Itms these metrics that probably make people reduce the number of authors. Yet, I think this is bs & as long as someone has made a genuine contribution they should be an author.
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Roland Hatzenpichler @environmicrobio.bsky.social · 24/07/2025
15 years later, finally, Science did the right thing at retracted the As life disaster paper! www.science.org/doi/10.1126/...
science.org
Retraction
The Research Article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. (1) has been the subject of discussion and critique since its online publication in 201...
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Alex Probst @alexjprobst.bsky.social · 18/05/2025
Take a photo with your iphone and you can copy from the photo! (it’s a 16S rRNA seq of an uncultivated archaeon)
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Bettina Siebers @bettinasiebers.bsky.social · 30/04/2025
For more information about the MEB team and the position, please visit: www.uni-due.de/umb/enzym_ho...
uni-due.de
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The Probst Lab @probstlab.bsky.social · 11/03/2025
Want to know who’s replicating and who’s just hanging out in your enrichment cultures? Our new study led by @soansi.bsky.social shows how @nanoporetech.com long-read sequencing can reveal replication states, shedding light on microbial growth. 🦠🧬 See our latest publication: doi.org/10.1093/isme...
doi.org
Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing
Abstract. Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous appro
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Alex Probst @alexjprobst.bsky.social · 11/03/2025
We never thought of giving the method a name. maybe we should have. the project went by the name „shit show“ though 😅
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Alex Probst @alexjprobst.bsky.social · 11/03/2025
😂😂😂
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Alex Probst @alexjprobst.bsky.social · 19/02/2025
I just submitted an article to a journal in under 10 min! I'm stunned that there are eventually submission portals that extract all necessary information (with AI?) from manuscripts when it comes to authors, affiliations, or funding statements. I'm impressed! (journal: Microbiome)
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FEMS Journals @femsjournals.bsky.social · 19/02/2025
🦠 #OilReservoirs harbor unseen microbial worlds! 🌍🔬 @alexjprobst.bsky.social lab study of a pristine reservoir reveals bacteria & fungi breaking down #hydrocarbons—and a global network of shared genes. But the mystery of plasmid distribution pattern remains! 🧬 #Biodegradation buff.ly/4gwdYUJ
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The Probst Lab @probstlab.bsky.social · 13/01/2025
We’re kicking off our Archean Park ERC project at @uni-muenster.de with @alexjprobst.bsky.social Jens Kallmeyer, Ivan Berg and Kai-Uwe Hinrichs & respective groups! Thanks very much to @donatogiovannelli.bsky.social and Prof. William Martin for giving invited talks to get us started!
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André Soares @geomicrosoares.bsky.social · 08/01/2025
Time's running out to apply for two PhD positions at the @probstlab.bsky.social ! Come do multi-omics bioinformatics of river microbiomes with us! 🧬💻🧬 Please RT!!
media.tenor.com
a close up of a red light that says alert
ALT: a close up of a red light that says alert
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cristinamoraru.bsky.social @cristinamoraru.bsky.social · 27/12/2024
Wanted: microbial ecology + bioinformatics enthusiasts for 2 PhD positions (@probstlab.bsky.social) #1 on microbial & epigenetic stress response in rivers tinyurl.com/bdf8eu5a #2 on virus-host stress response in rivers tinyurl.com/43cjd6es @alexjprobst.bsky.social @unidue.bsky.social
tinyurl.com
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Alex Probst @alexjprobst.bsky.social · 19/12/2024
#PhD #position #alert 2 bioinfo PhD positions @ProbstLab @RESIST_CRC #1 on microbial & epigenetic stress response in rivers tinyurl.com/bdf8eu5a #2 on virus-host stress response in rivers tinyurl.com/43cjd6es (supervision Moraru) Please share!
tinyurl.com
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Alex Probst @alexjprobst.bsky.social · 17/12/2024
Pls add! :)
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Alex Probst @alexjprobst.bsky.social · 14/12/2024
osf.io/preprints/os... almost identical to the final version
osf.io
OSF
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Axel Visel @axelvisel.bsky.social · 13/12/2024
We know they are major players in global carbon, nitrogen, and sulfur cycling 🦠 We can clearly see their fingerprints in metagenome data 🧬 And yet, just nobody can get ahold of them in culture 🧪 Join the hunt for the MOST WANTED uncultivated aquatic microbes. By @alexjprobst.bsky.social et al.
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Alex Probst @alexjprobst.bsky.social · 12/12/2024
-a 🤪
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Alex Probst @alexjprobst.bsky.social · 12/12/2024
Looking for a new target microbes for cultivation? Check out our new review on "Earth's most needed uncultivated aquatic prokaryotes"! www.sciencedirect.com/science/arti...
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Alex Probst @alexjprobst.bsky.social · 08/12/2024
I find the FISH images of the bacteria in the fish brain fishy. (lol) I do not see an image which clearly shows that the Eub338 signal aligns well with a distinct DAPI signal. I have my doubts…
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Alex Probst @alexjprobst.bsky.social · 07/12/2024
MEGWARE GmBH - 240 CPU nodes: 176x512 GB RAM, 51x1 TB RAM, 13x2 TB RAM - 19 GPU nodes: 17x4x NVIDIA H100, 2x2x NVIDIA H100 - Mellanox InfiniBand NDR200 Lustre file system 2,1 PB
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Alex Probst @alexjprobst.bsky.social · 07/12/2024
Grand opening of our new supercomputing cluster @unidue.bsky.social One of the front images features correlative microscopy by Indra Banas!
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