Alex Probst

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...

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 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

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!

Congrats, Ralf et al! :)

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.

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...

it was a pleasure, Gary!

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...

New paper alert with @alexjprobst.bsky.social.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

cool paper, congrats!
have you considered naming it under the @seqcode.bsky.social instead of calling it a Candidatus which has no priority?

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...

📢 🦠 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

Mein Beileid, liebe Sigrid. Fühl dich gedrückt.

I also got only one spot here… they are really rare unfortunately…

did you buy them or „hunt“ them? ;)

Congrats, Matt! Can‘t wait to see your latest results! Hopefully some new cool tools :)

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...

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...

#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...

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...

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.

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.

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...

15 years later, finally, Science did the right thing at retracted the As life disaster paper! www.science.org/doi/10.1126/...

Take a photo with your iphone and you can copy from the photo!
(it’s a 16S rRNA seq of an uncultivated archaeon)

For more information about the MEB team and the position, please visit:
www.uni-due.de/umb/enzym_ho...

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

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...

We never thought of giving the method a name. maybe we should have.
the project went by the name „shit show“ though 😅

😂😂😂

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)

🦠 #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
https://buff.ly/4gwdYUJ

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!

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!!

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