Big paper alert! This project has been years in the making. A comprehensive description of somatic mutation rates and signatures across 53 tissues or cell types using NanoSeq. A large collective effort led by Mimy Pham, Mike Stratton and @r-rahbari.bsky.social. www.biorxiv.org/content/10.6...

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune syst...

biorxiv.org

Glad to share StrainSpy, a new method developed by Sudaraka and co which identifies strain-level associations in metagenomics using ANI estimates from tools like Sylph. www.biorxiv.org/content/10.6...

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a s...

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 · last mo.

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

We are hosting the 2026 @abacbs.bsky.social conference at RMIT University City Campus Melbourne on 16-20 Nov 2026. Hope to see you there.

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

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...

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

👀👇 New work on sexually transmitting Shigella (press-friendly: bit.ly/4bBarEL) From continued collaboration with @clairejenkins2.bsky.social @ukhsa.bsky.social, @pducambridge.bsky.social co-lead @hsalje.bsky.social, a talented student Julia Marshall www.linkedin.com/in/julia--ma..., and others! 🧫🧬💊

The Lancet Infectious Diseases@thelancetinfdis.bsky.social · 2mo ago

New Research The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study www.thelancet.com/journals/lan...

Happy to share the latest work from Zunair Khurram, a PhD student in our lab! Zunair has developed a new method, MxSure, to infer within-host substitution rates and transmission thresholds from longitudinal isolate and metagenomic sequencing data. www.biorxiv.org/content/10.6...

MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds

Quantifying short-term evolutionary rates of microbial genomes is essential for understanding the processes that shape within-host evolution and for establishing thresholds needed to track transmissio...

biorxiv.org

Finally a preprint for our tool DAMPA (Australiana included) that generates efficient probe panels for targeted metagenomics from pangenome graphs. Presented at ABPHM and ABACBS last year. www.medrxiv.org/content/10.6...

DAMPA - accelerated and simplified design of probe panels for targeted metagenomics using pangenome graphs

Targeted metagenomics, where samples are enriched for multiple organisms of interest using oligonucleotide probes, is a highly efficient sequencing methodology that is becoming standard practice for g...

medrxiv.org

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

agtools: A Software Framework to Manipulate Assembly Graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

Sam Horsfield@samuelhorsfield.bsky.social · 4mo ago

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

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!!

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 9mo ago

High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1

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 🧬 🧪 💊

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation

Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

journals.plos.org

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...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

🧬 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

EMBL-EBI@ebi.embl.org · 10mo ago

Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care. EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform. #WAAW2025 #ActOnAMR www.ebi.ac.uk/about/news/t... 🧬💻

📣 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...

2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB)

Symposium Schedule All presentation times are shown in Pacific Daylight Time (GMT -07:00 / UTC -07:00) Time Talk / Session 9:00 Welcoming remarks by Sid Venkatesh Session One: Neural Effects

isbscience.org

“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