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Alex Probst

@alexjprobst.bsky.social
1.4K followers 598 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
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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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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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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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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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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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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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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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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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 · 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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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
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 · 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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Axel Visel @axelvisel.bsky.social · 11/11/2024
Here is a starter pack for anyone interested in environmental genomics: Members, users, and collaborators of the Joint Genome Institute @jgi.doe.gov Still many open slots, if you are working with the JGI and want to be added, DM me. go.bsky.app/7jENfK9
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Universität Duisburg-Essen @unidue.bsky.social · 04/11/2024
Eröffnung des Research Centers #OneHealth Ruhr durch Ministerpräsident Hendrik Wuest und NRW-Wissenschaftsministerin Ina Brandes! 🥳Hier werden die komplexen Wechselbeziehungen zwischen menschlicher Gesundheit und #Umweltgesundheit erforscht. #UARuhr www.uni-due.de/2024-11-04-e... 📸RUB/Katja Marquard
Ministerpräsident Wüst am Renderpult.
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Joint Genome Institute @jgi.doe.gov · 26/09/2024
Congrats to our Community Science Program Annual Call awardees! Recipients & collaborators include our Bluesky friends @alexjprobst.bsky.social, @cavenderg9.bsky.social & @andrewlhipp.bsky.social 🖥️🧬 Full list: jgi.doe.gov/announcement-fy25-csp-annual @axelvisel.bsky.social @lbnlbiosci.bsky.social
jgi.doe.gov
The JGI announces FY25 awardees for our Community Science Program Annual Call - DOE Joint Genome Institute
These projects include cutting-edge research into microbial communities — from freshwater estuaries reshaped by dam removal to Antarctica's photosynthetic mats — to reveal how these systems adapt and ...
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Alex Probst @alexjprobst.bsky.social · 15/01/2024
Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min anonymous survey here: shorturl.at/NOUW2 Please RT!
shorturl.at
Survey: “A roadmap for fair reuse of public microbiome data”
This survey will inform a manuscript titled “A roadmap for fair reuse of public microbiome data”, the abstract of which and core figure (Figure 1) are included below. The manuscript in its current...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 21/12/2023
Ten days remaining to apply to this exciting PhD position - join us in our quest to explore novel archaeal lineages!
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Panagiotis (Panos) Adam 🐐 @precambriangoat.bsky.social · 20/12/2023
New office! I can finally announce that I'm starting a new position next month as junior group leader at the Institute of General Microbiology at CAU Kiel. 1/4
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Chris Rinke @chrisrinke.bsky.social · 15/12/2023
Currently, we have the following open positions in the Rinke Group for Microbial MultiOmics and Biorecycling (MMOB) @ the University of Innsbruck, Austria: 1x postdoc 3x PhD 1x RA More info @ rinkelab.org/index.php/op...
Innsbruck, Austria
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The Probst Lab @probstlab.bsky.social · 12/12/2023
We are grateful for the privilege of hosting Sigrid Neuhauser @sigridneuhauser.bsky.social today. She delivered a fascinating talk about her work on Phytomyxids. As part of the university network AURORA she currently visits the ProbstLab to foster scientific cooperations. 🥬🧬🥦
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Alex Probst @alexjprobst.bsky.social · 12/12/2023
We are very happy to have @sigridneuhauser.bsky.social at our institute @unidue.bsky.social as an Aurora Professor to talk about her exciting research on eukaryotic microbes!
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Alex Probst @alexjprobst.bsky.social · 01/12/2023
Check out our new paper on low-input metagenomics with Nanopore. This was done on a mock community, application to real sample with actual research question in the works. Stay tuned for more fantastic work by Sophie Simon, grad student in our lab! link.springer.com/article/10.1...
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Jennifer Biddle @jenbiddle.bsky.social · 01/12/2023
New paper alert 🚨 We looked at methane fates in a salt marsh with an interdisciplinary team at UD: onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
High methane concentrations in tidal salt marsh soils: Where does the methane go?
Global Change Biology is an environmental change journal tackling issues such as sustainability, climate change and environmental protection.
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Alex Crits-Christoph @acritschristoph.bsky.social · 29/11/2023
The link above didn't work for me, here's a working link: www.biorxiv.org/content/10.1...
biorxiv.org
A rolling circle-replicating plasmid as an Inovirus phage satellite
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Holly Moeller @mixotrophe.bsky.social · 29/11/2023
I am *thrilled* to finally announce that our department is hiring an Evolutionary Biologist. We are esp looking genetic/genomic expertise, and those who can help us build a more equitable biology community at UCSB. Please apply by Jan 15! recruit.ap.ucsb.edu/JPF02635 #unicornjob
recruit.ap.ucsb.edu
Assistant Professor of Evolutionary Biology
University of California Santa Barbara is hiring. Apply now!
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 29/11/2023
Want to do a #PhD focusing on discovery, cultivation and characterization of novel prokaryotes? Come and join my group in the Laboratory of Microbiology at Wageningen University! Apply here: wur.nl/en/vacancy/p... #cultivation #microscopy #archaea #PhDposition Please share & repost
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Karthik Anantharaman @karthik-a.bsky.social · 28/11/2023
Reposting this message: I am looking to hire a lab manager/research technician for our laboratory. Please help us spread the word. If you know of any motivated candidates, please encourage them to contact me. Microbiology lab experience would be preferred. Looking for at least a 1.5 year commitment.
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Alex Probst @alexjprobst.bsky.social · 28/11/2023
Had a dream about the most annoying journal ever. It was called “Frontiers in MDPI”…
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Cameron Thrash @jcamthrash.bsky.social · 21/11/2023
Differential expression of core metabolic functions in Candidatus Altiarchaeum inhabiting distinct subsurface ecosystems www.biorxiv.org/content/10.1... #jcampubs
biorxiv.org
Differential expression of core metabolic functions in Candidatus Altiarchaeum inhabiting distinct s...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Matt Olm @mattolm.bsky.social · 22/11/2023
Excited to share our new technique for studying IgA binding in the microbiome! Fascinated by IgA since joining the Sonnenburg Lab, this work beautifully leverages Dr. Sean Spencers's immunology & my metagenomics expertise to make fundamental discoveries about IgA in the gut doi.org/10.1101/2023...
doi.org
Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Heal...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Laura Hug @lhug.bsky.social · 17/11/2023
New work from #HugLab, led by the ever impressive Dr. Daniel Grégoire (not yet on bsky)
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