Willem van Schaik

I definitely don't think this is a rare event per se, but Hi-C is almost certainly not the best technique to pick it up IMO

Headshot of Jeff Cole

We were deeply saddened to learn of the death of Professor Jeff Cole, a long-standing member who held many positions in the Society. Jeff was elected an Honorary Member in 2011. You can read his full obituary here: microb.io/46xYzkz

Check out some of the great work by @cynthiasilveira.bsky.social e.g. looking at Hi-C in marine environments pubmed.ncbi.nlm.nih.gov/39657233/

1908: the Lancet, one of the most respected scientific journals, calls for 18 age limit on reading in bed amidst a moral panic surrounding children becoming "addicted" to novels, which were "designed to keep kids hooked" and destroy their attention/mental health

If anyone is friends with any Georgian air traffic controllers, buy them a nice bottle of wine. As guardians of pretty much the only narrow gap still available between Europe and Asia that avoids both Iran, the Gulf, Ukraine and Russia, they are under some substantial pressure.

Amazing synthesis of microbial genomic evolution led by the top of the new talent on the block!

If there is a phage present at high level + many hosts that are being infected, you will probably see it in Hi-C, I agree. But this maybe uncommon in most environments, maybe in marine ecosystems more likely?

Completely with you that biology is weird and phages a different level of weird.

But it is unlikely to happen in many cells, in the same strain, at the same time, because that is what you will need, to detect it by Hi-C

In the Discussion of this paper we touch on some studies that are almost certainly interpreting noise as a signal.

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are lo...

I think Hi-C is unlikely to spot extremely rare events (e.g. the presence of non-replicating DNA inside a single cell in a community) so from that perspective most Hi-C links are probably 'real' (but with caveats re noise & bioinformatics: www.microbiologyresearch.org/content/jour...)

Great @imibirmingham.bsky.social seminar by the brilliant @josebengoechea.bsky.social who has uncovered another cool and important mechanisms in Klebsiella pneumoniae virulence (no spoilers because unpublished data)

Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occa...

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...

Really looking forward to this and also hearing all the other exciting talks! Big thanks again for then invite 😀

If you haven't watched 'Dirty Business' on Channel 4 yet, I highly recommend you do. Brilliant, angry TV.

🔔Seminar Opportunity🔔

We're looking for (self)recommendations for a Postdoc who is working in the area of AMR (any area, any discipline) to give an online seminar in May.

Reply, DM or email me, there will more opportunities in the future as well so will be good to have a list.

#MicroSky #AMR

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.

My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

Hang in there, your research is too important for the world right now.

That's a shame. Hope you will find a great place to move to.

Influencers in Dubai switching from “everybody should move here” to “this Is a crisis and the British government should get me out of here” without a single blink

Would you consider a move to the UK? My university is recruiting across all disciplines.

Treasury plans depend on net migration being much higher than current policy will deliver or current Home Secretary willing to accept.

Something will have to give. Will Labour deliver tax rises and spending cuts just before an election to keep net imm close to zero? Or let imm rise to avert this?

On app (Android): settings -> moderation

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

There is never a good time to watch Threads so may as well do it today

What is happening in US politics is awful, but in some way guards as a vision of what could be to come if we vote for authoritarian ideas in the general election.

Unfortunately the band is not named 'Having Fun Amid Family Drama'

No!

Amazingly, this is not satire!

Source: www.instagram.com/reels/DVMMed...

Terrible headline (this is NOT what the new research - link below - shows!), terrible AI image! Argh!
Here’s the actual research:
www.science.org/doi/10.1126/...

Where do I start?! 1/4

unsurprising though