Really pleased to share the first paper to come out of the lab. We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung. The phylogenies indicate that the clones moved from lung->gut www.nature.com/articles/s41...

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)! We're looking for someone keen on bioinformatics and microbiome evolution. Important info below on eligibility & URSA competition funding👇 www.findaphd.com/phds/project...

E. coli can spread as quickly as swine flu, new research reveals. 🦠 For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections. Read here ⤵️ sanger.ac.uk/news_item/ad...

I'm looking for a Doctoral Researcher (PhD student) to work with me on simulation-based inference at Data Science Research Centre, Tampere University Check the link for details and send an application before October 10th. tuni.rekrytointi.com/paikat/?o=A_...

Overjoyed to have received one of the FRIPRO Young Talent grants from the Norwegian research council to investigate the effects of hospitalisation on Klebsiella colonisation! 🎉🥳 www.med.uio.no/imb/om/aktue...

Congratulations to our own fantastic Jessica Calland @ocbe.bsky.social for receiving the prestigious FRIPRO Young Talents grant from the Norwegian Research Council! 🎉 She will continue her work identifying drivers of Klebsiella colonisation in critically ill patients. www.med.uio.no/imb/om/aktue...

New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo. We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries. www.biorxiv.org/content/10.1...

Join us in beautiful Oslo! Associate Professor @ocbe.bsky.social @uio.no Deadline May 18th www.jobbnorge.no/en/available...

🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉 @irenlohr.bsky.social @katholt.bsky.social genomemedicine.biomedcentral.com/articles/10....

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.

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...

We have a new preprint out! The title says it all.

🚨 We are hiring for a 3-yr PDRA 🚨 The Whelan lab is seeking a microbiologist interested in microbe-pathogen competition and use of a Drosophila melanogaster chronic infection model to investigate the cystic fibrosis lung microbiome. For more info check out whelanlab.co.uk & apply at the link below:

🚨An exciting #PhD opportunity in my group🧫 @UniSurreyBioSci with Linda Oyama @QUB to work on #phage modulation of the poultry #microbiome and suppressing AMR. Closing date for applications is 3rd Feb Apply here: tinyurl.com/y57huecd Please share!! #MicroSky #PhDSky #AcademicSky Details🔽

Want to do a postdoc in Oslo? We're seeking candidates for a four year postdoc position in causal inference/time-to-event analysis. Application deadline is January 31. See below for more information and feel free to take contact if you have any questions! www.jobbnorge.no/en/available...

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/...

Every year, >200K newborns die from sepsis. Our team used machine learning to develop a set of genes that can predict neonatal sepsis risk using at birth blood samples. www.thelancet.com/journals/ebi...

OCBE is preparing to leave the dark social media. To help you connect with our community here 🦋, me made a starter pack with present and past OCBE members, a list that will probably will grow soon 😊 go.bsky.app/6bqMnLQ

New tool from me: I wrote a local aligner that can do approximate reference-based alignment and find genes in a query microbial genome, without a separate indexing step or any temporary disk space usage. Written fully in Rust and there will be a browser version out later: github.com/tmaklin/kbo 1/3

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

New paper: we deep sequenced E. coli within-host diversity in ~900 people in Pakistan, and found massive diversity in E. coli from lineages that are somewhat uncommon in Europe 1/5 www.nature.com/articles/s41...

Our study on combining genomics with autogenous vaccine design to control Campylobacter in poultry is out today in npj Vaccines! www.nature.com/articles/s41...

Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients" www.science.org/doi/10.1126/... Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25): www.science.org/content/podc...

We are happy to have been selected by SMBE to host a satellite meeting on Pathogen Pangenome Evolution Between and Within their Hosts: smbepangenomes.bacpop.org We are expecting the meeting to be in Tokyo on 26-28th November 2024, save the date!

📣 PhD opportunity 📣 Come discover how longterm antibiotic use shapes the lung microbiome of people with COPD and how it contributes to antimicrobial resistance transmission between microbes! "Transmissible Antimicrobial Resistance in the Respiratory Microbiome" (1/n) #PhDSky 🦠 🧪

For those who missed it, this is our latest preprint on using genomics to develop autogenous vaccines to reduce Campylobacter ending up on our plates! www.biorxiv.org/content/10.1...