Dominique Chaput

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.
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Guidelines for preventing and reporting contamination in low-biomass microbiome studies Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

This is so cool! I love putting diatoms under SEM but didn't know about amoebae building themselves diatom shells. 🤯 Thanks for sharing!

We despise immigrants for not putting down roots, even as we make sure that it is impossible for them to do so. We do this because we have no idea what we want.

open.substack.com/pub/iandunt/...

Letter: We are not strangers Letter to the editor

“I woke up with a sense of dread…”

A moving, deeply personal account from an EU citizen in Cambridge on how Labour’s new rhetoric is shaking people’s sense of belonging.

Don’t miss this powerful open letter.

@eastangliabylines.co.uk @cambsforeurope.bsky.social

And to be clear, my colleagues who immigrated here to work in other roles - e.g. cleaning, catering, nursing - are far more integral to keeping the NHS running than I am. But no, apparently we're now 'cheap foreign labour' that's 'tearing the country apart'.

I'm one of those whose arrival here was part of 'a sordid chapter' in the UK's history. Gearing up to do more 'incalculable damage' in the NHS tomorrow by (checking diary) running a specialist diagnostic lab test that I set up to help clinicians treat desperately ill patients in ICU.

Very impressive, congrats!

The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health - Genome Medicine Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; ...

🧬 Out today 🧬 - our TyphiNET
#AMR surveillance dashboard for #typhoid

Use TyphiNET to view genome-derived data on global and national annual trends in AMR and circulating pathogen genotypes via any standard web browser.

genomemedicine.biomedcentral.com/articles/10....

About fifty years ago, NASA strapped a message in a bottle to a rocket and flung it into the deep dark
It wasn’t supposed to go this far, but it did. Long past its mission, it’s still out there so far away now that a simple hello takes a day to reach it, and another day to hear if it says hello back

📢 Webinar: Stand Up for Science – A Global Necessity

Scientific integrity is under threat, we must act. Join us to discuss how to protect research & academic freedom.

📅 7 March, 13:00 CET
🎙 @charlottemar.bsky.social, @kityates.bsky.social, @martinmckee.bsky.social

🔗 Register: shorturl.at/Bsk3i

Agreed, sequence databases appear robust thanks to the INSDC - a testament to scientists collaborating globally to share and preserve data. But the sequence search tool on ENA, at least, appears to rely on ncbi BLAST so we may need to consider local implementations if we lose ncbi.

No need for you to move anything, data from all INSDC members is mirrored across the consortium. If you search, e.g. ENA, you will find sequences originally deposited in GenBank. Quite a remarkable system, a testament to what can be done when scientists collaborate to share and preserve data.

Very cool - I've always used separate primers for each domain and then been frustrated that the relative abundances couldn't be compared. Also, great choice of acronym. 😁

Now over 900 signatures. Please keep signing and sharing to send a clear message to the Royal Society that we want them to stand up for values that we all hold dear: docs.google.com/forms/d/e/1F...

Agreed, thanks to everyone who organised and participated! Really fun to meet other R geeks 🤓. I learned so much and look forward to using the AMRgen package.

Use the Human Microbiome Compendium data!

We made the data and code available, & created a website and R package to navigate the compendium. Links:

- Website: microbiomap.org

- Data: zenodo.org/records/1373...

- R package: blekhmanlab.github.io/MicroBioMap/

- Code: github.com/blekhmanlab/...

Integration of 168,000 samples reveals global patterns of the human gut microbiome The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform Abstract. Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome

As the great migration from Twitter to Bluesky begins, I have created the "Clinical Microbiology" starter pack to help you find your colleagues. Please let me know if you would like to be added!

go.bsky.app/VTpSjBL