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Alex Probst

@alexjprobst.bsky.social

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

48 Posts1365 Follower597 Folgt
The Probst Lab@probstlab.bsky.social · 6mo ago

🤯 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.
The Probst Lab@probstlab.bsky.social · 12mo ago

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...

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.

nature.com

Roland Hatzenpichler@environmicrobio.bsky.social · 12mo ago

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

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.

tinyurl.com

Ecotoxicology lab RC One Health Ruhr@ecotox.bsky.social · 12mo ago

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...

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.

nature.com

Gareth (Gary) Trubl@gtrubl.bsky.social · 12mo ago

New paper alert with @alexjprobst.bsky.social. enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

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...

enviromicro-journals.onlinelibrary.wiley.com

Anne Daebeler@anne-daebeler.bsky.social · last yr.

📢 🦠 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

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...

biorxiv.org

Nature Microbiology@natmicrobiol.nature.com · last yr.

#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...

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...

nature.com

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

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...

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...

biorxiv.org

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

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...

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

doi.org

Alex Probst@alexjprobst.bsky.social · 2y ago

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)

André Soares@geomicrosoares.bsky.social · 2y ago

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!!

a close up of a red light that says alert

ALT: a close up of a red light that says alert

media.tenor.com

Alex Probst@alexjprobst.bsky.social · 2y ago

#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!

Axel Visel@axelvisel.bsky.social · 2y ago

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.

Alex Probst@alexjprobst.bsky.social · 2y ago

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...

Joint Genome Institute@jgi.doe.gov · 2y ago

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

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 ...

jgi.doe.gov