We investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41... A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo

Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome - Nature Communications

Authors present the EPithelial Isolate Collection (EPIC), a large skin microbiome culture collection, uncovering new species, widespread antifungal activity, and hidden biosynthetic diversity, reveali...

nature.com

ICYMI: New online! Multidisciplinary Delphi consensus statement on minimal standards for clinical metadata and end points in microbiome studies

AH-MAZE-ING

Jay Shendure@jshendure.bsky.social · 5d ago

Preprint: biorxiv.org/content/10.6... This is the product of many years of effort, and particularly amazing summer teamwork by Qi Yu, Haedong Kim, @seidels.bsky.social @cxqiu.bsky.social and many others from Shendure Lab & SeaHub (a @alleninstitute.org @biohub.org @uwmedicine.bsky.social colab) 2/n

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

Exciting collaboration with @annabiosys.bsky.social's lab just went online. @isbscience.org metaSPLiT: a fast, efficient, and relatively low-cost method for single-cell transcriptomics in the human gut microbiome. 👇

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5d ago

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.07.30.741866v1

The headlines are still covering the cyclosporiasis outbreak from lettuce, but let's talk about a different summer, long ago. The headlines in Bavaria would have called it "summer diarrhea" & it was killing babies. Enter our hero, Professor Theodor Escherich of the Julius Hospital, Würzburg.

This is so cool.

Stirling Churchman@stirlingchurchman.bsky.social · last wk.

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

The manuscript describing SimPhyNI is now published! www.microbiologyresearch.org/content/jour... A few updates since last post, including some method tweaks that improve performance and speed. Also even easier to run. Try it for your microbial GWAS or epistasis needs!

High-precision binary trait association on phylogenetic trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

microbiologyresearch.org

Tami Lieberman@contaminatedsci.bsky.social · 7mo ago

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

Colistin resistance-mediated lipopolysaccharide modification in Klebsiella pneumoniae modulates host inflammatory response https://www.biorxiv.org/content/10.64898/2026.07.30.741922v1

FEMS MICRO 2027 – Growing Microbial Futures ✨ Explore Ljubljana & the venue ✨ Submit a session proposal ✨ Save the date Be part of the conversations shaping the future of microbiology. Join us in Ljubljana next July and stay updated: buff.ly/5HEuk3g

Session proposals are now open for ASM Microbe 2027 ! asm.org/events/asm-m... If there is a specific topic or speaker you would like to see in Chicago, this is your chance (until Aug 12) ! This is for Micro Symposia and Hub Sessions, but my DMs are open if you have ideas for bigger AEM sessions

This is why they’re going after Dr Fauci: he impeded grifters

Aaron Rupar@atrupar.com · last wk.

Peter Navarro: "I had a million doses of hydroxychloroquine in warehouses as the defense policy coordinator that I was trying to distribute to hospitals. And Fauci got the FDA stop me from doing that."

🧬🖥️

Rob Edwards@linsalrob.bsky.social · last wk.

I've been using Sanger's Artemis to view #genomics since ... who knows (it was first published in 2000). It's still super useful, but getting harder to install. I vibe-coded a lightweight browser-only version that views #GenBank files: linsalrob.github.io/genbank_view... 🧬💻 #phagesky

🎉 New preprint. First piece of work from us looking at how Klebsiella spp. use gut microbiome-associated metabolites present in urine. Very much v1 but we wanted it out for feedback, and to support lead author @devarsh1917.bsky.social as he applies for PhDs. #microSky

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last wk.

Hippurate hydrolases encoded by Klebsiella pneumoniae and Klebsiella oxytoca are functional https://www.biorxiv.org/content/10.64898/2026.07.27.739834v1

All I can do to help in the present existential crisis of Britain's universities is reiterate my evidence to the Commons Education Committee. There isn't anything else.

Trying to sort out a problem caused by databases renaming bacteria wholesale and mostly underwhelming* culturomics papers. Aargh! (*Several of them are under "Expression of Concern" notices from what I can tell, but even if the papers are retracted the genomes will be available in perpetuity.)

Jeff Goldblum's Iconic Jurassic Park Quote

ALT: Jeff Goldblum's Iconic Jurassic Park Quote

static.klipy.com

‘Great Inventions, 1961’ Jodrell Bank Radio Telescope Artist: Robert Ayton

📢To every #STFC project or facility facing cuts: get in touch. 📊We need numbers, evidence and stories showing what the UK is losing: people, skills, innovation and partnerships. ✏️Write to MPs, brief journalists, speak publicly. Don’t wait for others. Every voice counts.🧪🔭 #UKRI #PPAN

And here's a second NYU postdoc job ad, where I'm looking for a candidate that is interested in working on the gut-brain axis: apply.interfolio.com/189975 please share 🙏

Earlier this year UKRI launched a funding call to invest £40M in ONE AI lab. www.ukri.org/opportunity/... For some unknown reason they decided to fund TWO AI labs at the cost of £60M. An extra £20M. Just found. That's the equivalent of 7 more years of Jodrell Bank. www.ukri.org/news/ukri-la...

UKRI launches two AI research labs to stay ahead in global race

Two new labs will back British researchers to develop next generation artificial intelligence (AI) systems, helping secure the UK’s position as a global leader.

ukri.org

Astronomer Royal for Scotland | Catherine Heymans@astroroyalscot.bsky.social · last wk.

I'm absolutely devastated for colleagues at Jodrell Bank who found out this morning that funding for the UK's e-MERLIN radio telescope array will be terminated. This is a short-sighted move, to save a tiny fraction of the overall UK science budget. #SaveJodrellBank 🔭🧪 www.bbc.co.uk/news/article...

Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

Delighted to have this collaborative work out in @natmicrobiol.nature.com on how A. muciniphila deploys its sulfatases, both their localisation and substrate specificity, to metabolise colonic mucin www.nature.com/articles/s41... #glycotime.

Unique adaptations in sulfatases underpin colonic mucin degradation by Akkermansia muciniphila - Nature Microbiology

Structural and biochemical follow-up of a serendipitous discovery reveals that Akkermansia muciniphila carbohydrate sulfatases are uniquely adapted to digest colonic mucins in collaboration with other...

nature.com

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

In addition to GC and strain bias, certain taxa showed systematically underestimated completeness via CheckM1 and 2, so historically much more likely to get erroneously thrown away in fragmented short read MAGs—a 3rd reason for the existence of Ghost Taxa. A sub-🧵. bsky.app/profile/stev...

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

@zaminiqbal.bsky.social Another publication that has benefitted from genomes available via AllTheBacteria.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3w ago

A capsule polysaccharide synthesis locus database for the Klebsiella oxytoca Species Complex https://www.biorxiv.org/content/10.64898/2026.07.16.739023v1

A capsule polysaccharide synthesis locus database for the Klebsiella oxytoca Species Complex https://www.biorxiv.org/content/10.64898/2026.07.16.739023v1

Prevalent glutamyl-endopeptidases in the commensal skin microbiome have itch-relevant activity https://www.biorxiv.org/content/10.64898/2026.07.17.739094v1

Check our preprint and this global effort "AllTheBacteria" to uniformly process all public bacterial and archaeal genomes and make them accessible, searchable and AI-ready.

César de la Fuente@delafuentelab.bsky.social · 2w ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

Dear predatory journal, you've clearly never met me and my RBF.