Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...

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)

Our new preprint on quantifying microbial sample diversity/complexity in a way that accounts for both metagenome architecture and taxonomic composition is now live on bioRxiv: www.biorxiv.org/content/10.6... #metagenomics #bioinformatics #dataanalysis #graphdata

Final version of our last paper is out! www.nature.com/articles/s41...

We’ve published a wee pilot study assessing the utility of metagenomics & full-length 16S sequencing for the detection of seasonal pathogens (and AMR) in our local urban recreational swimming hot-spot Check it out if you’re into that stuff :) www.microbiologyresearch.org/content/jour...

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover. 🔗 www.biorxiv.org/content/10.6...

Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics 📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing www.doi.org/10.1099/mgen.0.001644 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠

Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...

🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

🧬🖥️ I’m building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools Now looking for a few bioinformaticians for a brief usability feedback interview 👩‍💻 DM me or respond here if interested 👋

Me getting back to sending nagging emails on January 6th when people return to work from the Christmas break

New preprint to close out the year! Led by Alana Papula and together with Daniel Fisher, we used single-cell genomes to infer the evolution of Prochlorococcus—one of the most abundant and genetically diverse bacteria on Earth. Check it out here: doi.org/10.64898/202...

Rapid and Consistent Genome Clustering for Navigating Bacterial Diversity with Millions of MAGs and Isolates www.biorxiv.org/content/10.6... #jcampubs

New preprint modeling pathogen phylogeography, where infected hosts spread disease through short "trips" between locations. Very fun collaboration with the brilliant @albertchristian.bsky.social and Ammon Thompson. www.medrxiv.org/content/10.6...

Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2

Sharing a Shiny app I've been working on at @leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org. shiny.sph.cuny.edu/BugSigDBEnri... #rstats #microbiome #microbiomeresearch

A very cool app to compare a list of microbes with microbial signatures in BugSigDB and Bugphyzz 🧫 #microbiome

We’re excited to share our latest study that reshapes our understanding of Mycobacterium tuberculosis (Mtb) lipid composition, with major implications for drug discovery, immunity, and vaccine development. www.nature.com/articles/s41... A thread.

Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky

💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases. #bioinformatiocs #microbiology #genomics github.com/tseemann/mls...

Antibiotic-resistant typhoid infections are a growing global health problem, made worse now by emerging carbapenem resistance. tinyurl.com/4uy7f6y3 by Thirumoorthy et al.

🧬 #Bioinformatics AEGIS #PostdocJobs in metagenomic pipelines & HPC: Ancient Environmental Genomics at @ucph.bsky.social to reconstruct ecosystems and develop climate-resilient crops. 🌍 Deadline: Jan 4, 2026. Mikkel Winther Pedersen ([email protected]) #AcademicJobs #aeDNA #ClimateChange

New preprint from the lab is out! 🥳 We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions. www.biorxiv.org/content/10.6... 👇

Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪 www.nature.com/articles/s44...

Reading the structured abstract alone should set off a half dozen statistical alarms in any scientists head. The fact that this found its way into Science makes me wonder how we drive home those stats 101 lessons and make them intuitive. www.science.org/doi/10.1126/...

This paper by Celentano et al. on scalable simulation under the birth death is one of my favourites for the year! It introduces some elegant thinning that has been sorely needed. Fantastic to pave the way forward for future simulation-heavy inference, including neural Bayes! doi.org/10.1073/pnas...

I really love this model which brings real mechanistic insight to the barcode data which I had previously found interesting but mysterious! elifesciences.org/reviewed-pre...

We just posted a new preprint describing an anti-MRSA phage targeting the terminal β-GlcNAc on wall teichoic acid. The host becomes phage resistant, but methicillin susceptibility is the consequence in some pathways; cotreatment with methicillin is synergistic at achievable MICs. #phagesky #IDsky

#microsky #phagesky The 3rd (? Lost track!) manuscript on a CRISPR/anti-CRISPR -based transposon tool to study gene essentiality in #phages www.biorxiv.org/content/10.6...

We would be very happy to host a #bioinformatics #postdoc within this call! If you have expertise in #gutmicrobiota, #metagenomics, #machinelearning and/or #multiomics approaches, please get in touch to discuss potential 🧬& 🖥️ projects. Please share! @MicroSky www.scilifelab.se/data-driven/...

🌊 🐟🦭🐋🐧 I have a PhD position available (4 years, start Mid-2026) at NRM Stockholm to work on the macrogenomics of sea warming. Apply here: recruit.visma.com/spa/public/a... #PhD #MarineGenomics #ClimateChange #EvolutionaryBiology #PopGen #Bioinformatics #conservationgenomics

The 2025 #BacDive 🦠 release is now online. 🎉🥳 The database now contains information on more than 100,000 strains 🧫. For this update, new data provided by @leibniz-dsmz.bsky.social and information on type strains of newly described species from the #LPSN database were added.

#AMR #Klebsiella cause >100,000 neonatal deaths globally each year. Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW doi.org/10.1101/2025...

A last thought before taking off into your various breaks - Microbial Genomics is looking for editors! Scientific publishing is frustrating and so much money going to commercial publishers... be part of the change by supporting society publishing 😊 great opportunity to join a lovely community.

AI folks now having to realise what GWAS folks did about studying bacterial genome datasets. Great work by great researchers

(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪

We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬 Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions) (1/7)

Genetic diversity and antimicrobial resistance profiles of Salmonella enterica in the broiler supply chain in Harare, Zimbabwe: tracking transmission from farm to table. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen... #MGen

Wow this is a seriously serious supplementary figure from @cellpress.bsky.social today. Panels A through UU. I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here? www.cell.com/cell/fulltex...

I am still actively looking for postdoc positions — please lmk if you (or your friends and colleagues) need a hardworking postdoc with field, lab, and bioinformatic skills! I am broadly interested in evolution in the ocean, conservation and population genetics, and rapid evolution.

Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/

GSC: efficient lossless compression of VCF files with fast query academic.oup.com/gigascience/... 🧬🖥️ github.com/luo-xiaolong...

As 2025 wraps up, we’re looking back at some of the most intriguing microbes that made their scientific debut this year. This blog highlights standout bacterial species that caught our eye. Read the full #FEMSmicroBlog: buff.ly/2wz7k16 #NewMicrobes

We're excited to share our lab's first lead paper! We developed OriGen, a language model trained to generate plasmid origins of replication. 🔄🦠 The model generates sequences that are significantly different from wild type origins and, remarkably, they allow for replication in vivo. Read it here ⬇️

A very nice Preview of our work in @cp-cellhostmicrobe.bsky.social this morning from Chrishan Fernando & Nicole D. Marino! www.cell.com/cell-host-mi...

Our new Microbial Primer describes the mechanistic action and therapeutic potential of R-pyocins produced by P. aeruginosa. www.microbiologyresearch.org/content/jour...

#microsky #phagesky Gut #phage biobank www.nature.com/articles/s41...

Very happy to see this remarkable work published. Led by @tommclean.bsky.social and @ainsley-beaton.bsky.social. We show how Streptomyces bacteria sense & respond to misfolded secreted proteins. A great collaboration with @barriewilks.bsky.social #microsky 1/2 journals.asm.org/doi/epub/10....