New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome. 🔗 biorxiv.org/content/10.1... A short thread (by Juliane Weller)👇

Showcase advances in infection and respiratory immunology at our 2026 conference! Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders. 🗓️ #AIR2026 dates: 11-13 February 📩 Submit an abstract by 17 November 📎 bit.ly/46T6uJB

Interested in respiratory infections? who isn't! Then register for this fab conference with a fantastic line-up of speakers and sessions @sangerinstitute.bsky.social Abstract submission open until 17th Nov!! @eventswcs.bsky.social coursesandconferences.wellcomeconnectingscience.org/event/air-20...

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers. 🚨 Submit your abstracts now! 🚨 Please RT coursesandconferences.wellcomeconnectingscience.org/event/air-20...

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research microbiologysociety.org/news/society...

RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon

BBSRC Fellowships 2025 Triage Outcome Decisions were today. 277 applications, 42 put through to peer review and interview. A fellow I was supporting didn't get selected and BBSRC now offer *no feedback*. Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.

Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post

Now published, our tool to run (almost) all biological models interactively in your web browser Paper: academic.oup.com/bioinformati... Website: biomodels.bacpop.org Code: github.com/bacpop/SBMLt...

Synthetic lethal TN-seq! #microsky 🦠

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

It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...

Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦 Key takeaways: 🔹 Host ancestry + diet shape Bif evolution 🔹 Mammals enriched for carb-busting enzymes 🔹 Untapped diversity in non-human hosts = new probiotic potential

Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB

Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...

Super interesting. Does it work for NTM?

Be thAIR or be squAIR (My second entry into the organising committee pun competition. A winner there I think).

Early notice of NEW Wellcome Conference - AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity 11th-13th February, sign up below for notifications coursesandconferences.wellcomeconnectingscience.org/our-events/c... It's immunulogy AND it's microbiology 🫁

⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco... I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u... Please reach out!

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference www.nature.com/articles/s41...

Great faculty opportunities within the Cellular Genomics Programme @sangerinstitute.bsky.social Please share with your networks and do contact me if you would like to find out more sanger.wd103.myworkdayjobs.com/en-US/Wellco...

New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs. Take home message: don't use the word "Delve" www.science.org/doi/10.1126/...

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)

Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11 www.medrxiv.org/content/10.1...

I am excited to begin my new journey as the Head of Cellular Genomics @sangerinstitute.bsky.social We will decode and recode tissue ecosystems using AI + big data… Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..

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!

New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...

Happy to share our first preprint looking at the nasal microbiome in ~1000 healthy adults from the CARRIAGE study of 20,000 healthy blood donors to understand nasal colonisation by Staphylococcus aureus. Ten years in the making! doi.org/10.21203/rs....

Scientists in Beijing built a 10¢ test that detects Covid in under 1 minute—faster, cheaper & more sensitive than PCR or CRISPR. No machines, no enzymes, no labs. Just flip a test tube and read the result, similar to a pregnancy test but faster & more sensitive. www.science.org/doi/10.1126/...

Interesting. A 57-codon genome. www.biorxiv.org/content/10.1...

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

Out now in Cell! Thrilled to share our recent study on global analysis of microbial genetic diversity in geography and human health. Congrats @seandreu.bsky.social and all other co-authors. Special thanks go to @cibiocm.bsky.social and lifelines.

Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander www.biorxiv.org/content/10.1...

B͓̊å͓c͓̊t͓̊e͓̊r͓̊i͓̊å͓l͓̊ s͓̊ů͓g͓̊å͓r͓̊ f͓̊ů͓e͓̊l͓̊s͓̊ c͓̊å͓n͓̊c͓̊e͓̊r͓̊ r͓̊i͓̊s͓̊k͓̊ Study in 𝘕𝘢𝘵𝘶𝘳𝘦 finds ADP-HEPTOSE, a bacterial sugar produced by Gram- gut flora, leaks into the bloodstream with age, activating NF-κB, giving pre-leukaemic blood cells a growth edge, and triggering dangerous clonal haematopoiesis Starczynowski Lab U Cincinnati

1 hour lab-in-tube assay for TB! "point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure" www.science.org/doi/10.1126/...

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

1 week until deadline for this postdoc position. Really key position in my lab working on amazing datasets

Cecilia Kyany'a will be presenting our very cool work applying spatial transcriptomics to mycobacterial infections at 12.10 in the infection forum #Microbio25

Genome Science UK 2025 - 9th-11th July - Newcastle www.genomescience.org.uk There's a great programme developing - covering Microbial / Plant / Animal / Human #Genomics with a major focus on emerging and transformative technologies!

We published a cool new paper showing that some M tuberculosis lineages (mainly L1 and L6) seem less transmissible but that's mainly because they have longer initial non-infectious 'latent' periods. www.sciencedirect.com/science/arti...

Excited to share our last study. Huge congrats to Sarah Monard, Arnaud Métais, @gclugo.bsky.social, @chrisverollet.bsky.social and all colleagues! We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell. Let's dive in👇 shorturl.at/x4Sb5

If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc: sanger.wd103.myworkdayjobs.com/WellcomeSang... Incredibly exciting datasets on host-microbe interactions in the lung. Pls RT and reach out if you are interested.

Given hyperbole about this paper www.nature.com/articles/s41... in the news today (eg www.bbc.co.uk/news/article...) it is a good day to post this classic from >20 years ago: www.microbiologyresearch.org/content/jour...

I’d like to think I’m the first person to get into a flame war with VPOTUS from the swimming pool of Woburn Center Parcs at half-term.

Any suggestions for tracking worms like C.elegans and other things from live imaging fluorescence data? Would like an open source tool.

For a palate refresher, please enjoy @quevan.bsky.social 's thread on our latest preprint. I'm really excited about PHLAME's ability to get precise strain level, evolutionary contextualized, information out of difficult sample types (like the skin microbiome, where many strains coexist).

We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church. www.science.org/doi/10.1126/...

Smoking costs society in England £43.7bn a year through a combination of lost economic productivity and health and social care costs. This rises to £78.3bn if the cost of early deaths due to smoking is included. ash.org.uk/health-inequ... @ashorguk.bsky.social #RespEd #LungSky 1/n

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/... #microsky #microbial #microbiology #genomics #transcriptomic 🦠🧫

Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3 @fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social