Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

QUESTION: anyone knows of a published example of a gene/operon which is toxic in Pseudomonas aeruginosa if in high copy plasmids, but ok in low copy? Got plenty of examples of my own for E. coli (esp of membrane protein genes), but struggling to find for Pae… Cheers! #microsky #synbio

To maybe spare someone else the headache I just went through trying to figure out why I couldn’t find any NCBI assembly tables letting me parse by “representative” genomes, they purged the term last year and solely use “reference” now. #MicroSky

Many studies have shown that there is no relationship between MMR vaccine and the development of autism. Here are two of the best. This one followed every single child born in Denmark from 1991 through 1998 (n=537,303). There was no association.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

It's like you can see the interaction between ecology and evolution happening right in front of you. 💚🦠🧬 #mevosky #bluesci www.science.org/doi/10.1126/...

Happy to share that the 1st chapter of my PhD on how coastal & oceanic Synechococcus deal with iron × warming interactions is now published in Environmental Microbiology Reports! enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Here at STAMPS 2025 we will be using bluesky and specifically #stamps2025 to social-media-ify our teaching on microbiome data analysis techniques! cc @amydwillis.bsky.social

New blog post I wrote on 'how we do not choose our families but we can choose people who push us', and ONLY for my scientist colleagues who are looking for things to procrastinate with style (by requiring them to be longer than a post on BlueSky) :p merenlab.org/2025/07/16/s...

Tomorrow at 12:45-1:30 in the EEB Track Hub in the poster hall #ASMmicrobe I am talking about microbial diversity including Asgard archaea, and an expanded tree of life from marine sediments.

Awesome! 🦠

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

This is an amazing group to work with! 🦠

Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...

For people with hmmalign experience. When running post-alignment trim (i.e. clipkit/trimal), how do you handle insertion gap added by hmmalign? AFAIK many trimmers don't count '.' as AA gap character - and manually adjusting '.' to recognized gap character can significantly alter results 💻🧬🦠🧫

Pseudomonas aeruginosa clinical isolates can encode plastic-degrading enzymes that allow survival on plastic and augment biofilm formation This strain encodes a polyesterase that degrades polycaprolactone, and it can use it as a sole carbon source: www.cell.com/cell-reports...

Strain-level metagenomic profiling using pangenome graphs with PanTax #MicroSky

This is important work for the exciting next stage of metagenomics #MicroSky

Super cool! #MicroSky

Happy #Caturday 😺

🧪This mesmerizing green and purple cloud happens inside our gastrointestinal tract everyday! Swimming bacteria use chemotaxis to rapidly find nutrients. Takes only a few seconds. WAY faster than phagocytes (~20 min). Bacteria will literally swim circles around them 🦠💨 #MicroSky #IDSky #GastroSky

Biology is so cool - P. syringae produces syringafactin, which is deacylated by amoebae - Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis - Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae #MicroSky

The first #anvio workshop at our brand new @hifmb.de building in Oldenburg has just started with around 50 individuals who represent a wide range of locations, scientific interests and career levels :') Very excited for this week and thankful for Iva Veseli and Florian Trigodet!

One cannot simply *stop developing* SPAdes :)

It’s a cliché to say it—and no two historical scenarios offer a perfectly compelling analogy—but what each American is doing now is what they’d be doing were they a German living in Germany and were it 1936-38 There’s no more doubt about who the appeasers or the bad guys are—they’re in the open now

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data www.biorxiv.org/content/10.1... #jcampubs

70% of an E. coli cell is water. The other 30% of mass is *mostly* proteins. But what's the most abundant protein in the cell? To my surprise, it's Lpp, a protein that anchors the outer membrane to the peptidoglycan layer. There are ~700,000 of them in each cell. New blog🔻

Is the communications pause that's been imposed on the US government's health agencies affecting you? @statnews.com would love to hear about it. Please let us know. www.statnews.com/2025/01/25/t...

1/2 Happy to announce EvoQuant LLC is launching consulting services (boinformatics and more) starting Jan 1, 2025 See our new, preliminary, website at: evoquantbio.com #Bioinformatics #SoftwareDevelopment #DataScience #Python #R #Nextflow #AWS #GCP

Out now in @genomebiolevol.bsky.social! With colleagues at NBACC and PNNL, we helped answer a long-standing question about how widely-divergent cyanobacteria produce saxitoxin, a major cause of paralytic shellfish poisoning. We assembled a new genome for a producer of saxitoxin and ...

Snow day!

Pretty sky tonight too with the moon and Venus snuggling up in this Maryland snow 🌨️

Beautiful sky this morning 👀

We're hiring two bioinformatics-focused PhD students - one on microbial & epigenetic stress response in rivers, another on virus-host stress response in rivers! 🧬🦠💻 @unidue.bsky.social @cristinamoraru.bsky.social Please RT & spread the word - the @probstlab.bsky.social awaits you! 🦸 @idw-online.de

Where the microbes aren't academic.oup.com/femsre/advan... #jcampubs

No only is this being led by some incredible people, but anvio is a super-empowering platform for microbialomics! If this is interesting and doable for you, I promise it would be worth it! 🦠

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What kills us now and in 1900. In 1900 most people died of infectious diseases that are now preventable or curable with vaccines and antibiotics Covid-19 was the first pandemic in a century, but wont be the last, to remind us that infectious diseases are not gone. Pandemic preparedness is key. 🧪🦠

An opportunity to work at an amazing place with amazing people! 🦠 “GeneLab is seeking a #Bioinformatics #ProgramDeveloper to drive research with #omics data from space biology experiments. Develop workflows and analyze data critical to human space exploration. 🔗 Apply now: tinyurl.com/8psb8uwn “

Very excited to present our latest work as my first post on Bluesky. Thanks to all co-authors for their valuable contributions! A truly mammoth effort with many different fields of expertise coming together. Looking forward to working with all of you in future as well. #Microsky

Quick (re) introduction. My name is Thomas, and I work at @unidata.bsky.social bringing ML education into the classroom and virtually! I am a co-PI on a NSF CyberTraining grant that is wrapping up next year. I will be at #AMS2025 if anyone has any questions or wants to chat!

We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster! LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes! We'll provide an index for ATB on AWS later. github.com/shenwei356/L...

I just wanted to send a quick update and thank the 70+ people who applied for the upcoming #anvio workshop and ECR symposium in Oldenburg so far. We are very encouraged with the geographical diversity, which has been one of our main concerns. The applications are open until January 10.

News on ribosome hibernation 🦠 #rnasky #microsky Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins: Structure www.cell.com/structure/fu...