Jo Herbert

www.genomeweb.com/sequencing/o...

I guess the complaining worked a bit!

This is true, I have only recently moved to being in charge of ONT machines and I had no idea there is an annual fee……

But the P2i move is ridiculous

As someone using the P2 Solo in an academic setting I was also really disappointed in that announcement. I am a huge advocate for ONT but I’m really sad they’re moving away from affordable sequencing :(

📣I’m recruiting a postdoc to join my team in the new Center of Excellence in Peatlands, Climate Change and Ecological Restoration (PeatResC) at @aalto.fi . Theme: remote sensing of peatlands. Read more about the job here: www.aalto.fi/en/open-posi...

Extremely chuffed with the first direct RNA sequencing run last week 💪 VERY excited to look at the data 📊

💾 Prokka 1.15.6 is released!

This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics

github.com/tseemann/pro...

The position is still open.
Please apply here:
jobs.bc.cas.cz/en/detail/277

🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)

An Asgard archaeon with internal membrane compartments

Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!

www.biorxiv.org/content/10.1...

Variations in the latitudinal diversity gradients of the ocean microbiome Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...

Interested in how microbial #diversity is structured across the global #oceans?

Check out our newest preprint!
We show that latitudinal diversity gradients are taxon-specific, reflecting differing ecological strategies and their responses to environmental gradients

www.biorxiv.org/content/10.1...

Things you love to see on a Friday afternoon 💚 🧬

This is wonderful to play with, highly recommended for anyone who wants to understand the BWT

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Autocycler: long-read consensus assembly for bacterial genomes AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

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

Huntington's disease successfully treated for first time One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.

This is amazing science news.

'The therapy uses cutting edge genetic medicine combining gene therapy and gene silencing technologies.'

www.bbc.co.uk/news/article...

Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils www.biorxiv.org/content/10.1... #jcampubs

🦠Exciting PhD opportunity @ ETH Zürich!
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.

🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁

New preprint: Antimicrobial Resistance Cartography — a simple way to map multivariate drug-resistance phenotypes, using data from @CDCgov.

www.biorxiv.org/content/10.1...

🚨 PhD position in a great lab!

I can highly recommend working in Lucy’s lab, I did my Masters with her and it was an amazing experience (even through the Covid pandemic!)

🧬 🧫 🐷

Join us at the University of Portsmouth on Tuesday, 17th September for a public lecture titled "What has DNA ever done for us?", presented by Professor Sam Robson. Register here: www.eventbrite.co.uk/.../what-has....

First talk at ETH, presenting some of our new work using @nanoporetech.com at the GDC Symposium 🧬

It was a pleasure ✨

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

PhD Position in Environmental Microbiology

🚨 We are looking for a PhD student to join the ETH Environmental Microbiology Group, working on one of our peatland projects!

If you are interested in a position which involves fieldwork, lab work and bioinformatics then this could be for you! 🧬 🦠

Deadline: 03/10/25

jobs.ethz.ch/job/view/JOP...

Assistant Professor (Research and Education) in Bacterial Genomics at University of Birmingham Looking for a new job opportunity in academia? Check out this job opening for a Assistant Professor (Research and Education) in Bacterial Genomics on jobs.ac.uk!

Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!

@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...

This image is figure 1 which shows how changes in abiotic and biotic characteristics inform the progression of cocoa bean fermentation.

A community of microorganisms that can reproduce the flavour attributes of premium chocolate, by fermenting cocoa beans, are reported in Nature Microbiology. go.nature.com/4mH9uOo 🧪

Colorful mural painted on the side of a building with the likeness of Henrietta Lacks and the words “HeLa” and “Middle East” on it.

Beautiful mural honoring Henrietta Lacks painted by Baltimore community members popped up near Hopkins med campus recently.

Deep learning reveals antibiotics in the archaeal proteome - Nature Microbiology Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising ...

#NewResearch

Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising source of future antibiotics.

#MicroSky 🦠💉🤖

www.nature.com/articles/s41...

Archaea produce peptidoglycan hydrolases that kill bacteria Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...