ggCallaroo v0.1.0 is now out! This snakemake pipeline predicts, clusters and annotates bacterial genes using ggCaller, Panaroo and Bakta. It generates Panaroo files with functional annotations already integrated, which can then be used with the usual downstream tools. github.com/samhorsfield...

We’re hiring! Postdoc position at APC/School of Micro, working on gut microbiome–pathogen interactions in an ERC-funded project with @hilarybrowne.bsky.social 🧫 Anaerobic microbiology + bioinformatics 📅 Deadline: 17 April 2026 📰 Apply here: buff.ly/IxGKwH6 #Microbiome #Postdoc #AcademicJobs

Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes. www.biorxiv.org/content/10.6...

Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)

@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n

It's a bit last minute, but we have an RA/junior postdoc position available in my lab (closing Sunday). Please reach out if you're interested in developing and applying methods to analyse microbial genomes and metagenomes! careers.petermac.org/job/MELBOURN...

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

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!!

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…

PeterMac @petermaccc.bsky.social representing at #abacbs2025 What a community 😍

Great talk from Michael Payne at #ABACBS2025 on DAMPA - tool for designing probe panels for targeted metagenomics using pangenome graphs! Captures all diversity efficiently, uses fewer probes than competitors. Critical for syndromic surveillance! 🧬🔬 #Metagenomics

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

📣 Join us for the 2025 @isbscience.org Virtual Microbiome Symposium, focused on "Gut Microbial Metabolites and Their Impact on Host Systems". co-director - @flash-point.bsky.social 🦠💥 It's free, & we have an amazing line-up of speakers! Dec. 12th. Please share! isbscience.org/2025-isb-vir...

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Happy to see that Spacedust is now published on Nature Methods! It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes. 1/6🧵

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome. A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants. 1/2

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025. Check it out and share widely: www.abacbs.org/abacbs2025 Registrations and abstract submissions open next week, with abstracts due in August!

Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec? Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together! www.mcgill.ca/gps/funding/...

www.bath.ac.uk/jobs/Vacancy... Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug... For queries, email me!

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology www.nature.com/articles/s41...

Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.

We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in Melbourne, Australia 🔬🦘💥 Work in a cutting edge research environment in a vibrant world city! We value research excellence, creativity and diversity. Join us! careers.petermac.org/job/MELBOURN...

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1

How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own! medrxiv.org/cgi/content/...

Super excited that our JPIAMR grant on Candida has been funded 🙌https://www.jpiamr.eu/projects/fugaci/ Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!

Always exciting to see journals publish negative results on the microbiome! www.cell.com/med/fulltext...

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

This is amazing and important work by Glen Carter and colleagues at the University of Melbourne 'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus' www.nature.com/articles/s41...

Our study on the (huge) variations in transformation rates is now out in OA! Key question: why are so many strains non-transformable if the many recent transitions to non-transformability seem deleterious? doi.org/10.1371/jour...

Our metagenome profiler sylph is now published in Nature Biotechnology! (www.nature.com/articles/s41...)

There is still time to register for our SMBE satellite meeting on pangenomes and transmission in Tokyo (until 31st October) See our website for more details, and now a provisional schedule too! smbepangenomes.bacpop.org

One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org A new, open-source database for pathogen sequence sharing. 👐🧬🌎 1/12

Happy to share the preprint for our strain transmission inference method recently renamed to TRACS! www.biorxiv.org/content/10.1...

We are on the look out for postdocs to join the Lieberman Lab at MIT. Areas include: -Connecting bacterial warfare to strain dynamics in vivo -Evolution and transmission of microbes in humans -Revisiting role of microbes in acne vulgaris Take a look at our recent preprints and reach out!

Registration and abstract submission for our SMBE satellite meeting (Tokyo 26-28th Nov) is now open! Abstract submission closes on 31st August Registration is open until 31st October See our website for full details including confirmed speakers: smbepangenomes.bacpop.org

This 2020 paper on the cancer microbiome from Rob Knight's group has been retracted: www.nature.com/articles/s41... Per x.com/matthewherpe..., the authors agreed to the retraction, glad to hear they did so! There's still a *lot* of interesting stuff to grapple with here largely left unsaid 1/n