We have a fully-funded PhD studentship available to elucidate the host-adaptive traits of the human gut microbiome: bbsrcdtp.lifesci.cam.ac.uk/how-apply (targeted project: TRG-VET-AA26). Feel free to reach out with a CV and cover letter stating your interest in this project.

Applications to our free course on "Introduction to Experimental Design and Core Statistics" closes this Friday. Part of the @ukgibanetwork.bsky.social, this is a great opportunity to improve your statistical skills and get to meet other network members. Apply here: forms.office.com/e/sdys5HATUH

Applications to the first training event: "Introduction to Experimental Design and Core Statistics" of the UK GIBA Network+ (@ukgibanetwork.bsky.social) are now open! Taking place Dec 8-10 in Cambridge. Further info: www.giba-uk.org/training-opp... Apply here: forms.office.com/Pages/Respon...

📊 Want to boost your research skills? Join our 3-day training on Experimental Design and Core Statistics in Cambridge (Dec 8–10). ✅ Free to attend 🙋‍♀️ Open to all career stages 🚆 Travel and accommodation costs reimbursed Apply by October 17th 👉 www.giba-uk.org/training-opp...

Our working groups support the development of effective collaborations across the UK to advance research. Introduced by Franziska Denk (@denklab.bsky.social) at our #GIBANetworklaunch. Want to know our first 5️⃣ topics? Find out here 👇 www.giba-uk.org/working-groups

✔️ Flexible funds ✔️ Fellowships ✔️ Mobility awards Our director Jonathan Swann shares some of the ways we will expand the mechanistic understanding of the gut-immune-brain axis. More details will appear on our Network website in the coming days 👇 www.giba-uk.org/funding-oppo... #GIBANetworklaunch

“One of the key pillars of our network is training,” says @alexmsalmeida.bsky.social. We are committed to equip our members with the skills, tools and methods essential for research. Our first course was announced at our #GIBANetworklaunch 🌟 Want to know more? 👇 🔗 giba-uk.org/training-opp...

Representing the bioinformatics crowd at the #GIBANetworklaunch

The past two decades have seen a global explosion of research into the gut-immune-brain axis. There is great energy in #Southampton today for our #GIBANetworklaunch. Together, we are building a vibrant and diverse research community to fully realise GIBA's potential. Learn more 👉 www.giba-uk.org

🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...

The GIBA network will be launching on September 22nd with an in-person event in Southampton. Do come along to hear and share your thoughts on our plans to drive innovation in the gut-immune-brain axis field in the UK. Sign-up here: www.eventbrite.com/e/uk-giba-ne...

A new UK research network supported by UKRI will investigate how gut health impacts the brain, immune system, and mental wellbeing. Dr Alexandre Almeida (@alexmsalmeida.bsky.social) is part of the interdisciplinary team leading this new initiative. Read more: www.bio.cam.ac.uk/news/cambrid...

We're delighted that researchers from the @camvetschool.bsky.social are contributing to this important new network, advancing understanding of the gut-immune-brain connection.🧠👇🏽

Excited to be part of the leadership team of a new @ukri.org BBSRC Gut-Immunology-Brain Axis (GIBA) Network+ to drive further mechanistic understanding of the GIBA. See more: www.bio.cam.ac.uk/news/cambrid.... @camvetschool.bsky.social @cambridgebiosci.bsky.social

argNorm is published now academic.oup.com/bioinformati...

Me and a few of my mates got together and wrote a review on the current state of clinical translation of microbiome research. A great summary of the state of the art for microbiome research. www.nature.com/articles/s41...

Everyone thinking of using MR for microbiome studies should read this! So many microbiome MR work is published w/o any validation😠 Here, Kaitlin Wade et al. explain (very well!) that a good MR result can be inconclusive after appropriate subsequent sensitivity checks 🔗 www.nature.com/articles/s41...

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

New to bluesky - would appreciate a "retweet" please, so I can find everyone from twitter.

An in-depth analysis of 12,000 metagenomes looks at Enterobacteriaceae interactions in healthy humans These findings from @alexmsalmeida.bsky.social et al. highlight the critical role of the intestinal milieu in the colonization success of opportunistic pathogens

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/...

Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors A 🧵 1/10 www.cell.com/cell/abstrac...

New #MicrobiomeDigest is OUT microbiomedigest.com/2025/01/16/j... • Enterobacteriaceae in the human gut / @alexmsalmeida.bsky.social • microGalaxy / @bebatut.bsky.social • bacterial vaginosis /‬ @mikeusyk.bsky.social • invitation for the next week @microbiomevif.bsky.social & more. Happy 2025!

🆕 Blog! Our experts Prof @mjpallen.bsky.social Dr Falk Hildebrand @bioinf.bsky.social and Dr Aimee Parker explain that there is no evidence for a brain microbiome 🧠 https://buff.ly/40gVxNH

A paper in Nature Microbiology underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies. https://go.nature.com/4hgvQDA 🧪

🎉Huge congrats to @alexmsalmeida.bsky.social ‘s team on this fantastic publication! Honoured to have made a (tiny) contribution to our *first* work as collaborators. Here’s to many more 🥂🚀 @camvetschool.bsky.social @naturemicrobiol.bsky.social

OUT NOW - Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations www.nature.com/articles/s41...

Interested in the ecological dynamics of Enterobacteriaceae across populations? Check out our new study 🧬

Very interesting study! Must read for everybody working on enterobacterales!

Well done @alexmsalmeida.bsky.social and team on this next work on Enterobacteriaceae colonisation!

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

Great to get this out before the holidays: Integration of metagenome-assembled genomes with clinical isolates reveals genomic signatures of Klebsiella pneumoniae in carriage and disease (www.biorxiv.org/content/10.1...)

We are thrilled to see 3 projects in the School receive funding from this call – congratulations to Alex Almeida (@alexmsalmeida.bsky.social), Charles Emogor, Máiréad Healy, and Zoe Kourtzi!

Really grateful to @acceleratescience.bsky.social for funding our project on combining AI and metagenomics to improve pathogen tracking. Look forward to getting started on this next year!

International consensus statement on microbiome testing in clinical practice - just out in Lancet Gastro & Hepat www.sciencedirect.com/science/arti...

I thought we learnt an important lesson during the pandemic - preprints should be taken with a grain of salt. I thought we did. www.theguardian.com/lifeandstyle...

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

Today we publish an (in my opinion) important paper in @naturemicrobiol.bsky.social 🍾 showing that gut physiology and environment are factors explaining substantial variations in human gut #microbiome composition and #metabolism🦠 Fantastic work Procházková et al. 👏 www.nature.com/articles/s41...

I often get asked what is the best place to start to learn more about the human microbiome for those new to the field. I always default to this excellent collection that was put together by @npariente.bsky.social and Ashley York: www.nature.com/immersive/d4.... Any other good recommendations?

With all the doom and gloom about the use of AI, the potential benefit of these technologies for improved health should be better conveyed to the general public

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024... @wwood @rhysnewell @CMR_QUT 🧵1/6

Delighted to see this out, after a 2-year-long review process that left @drsimonmcarthur.bsky.social and I wondering what we'd done to upset the reviewing gods. #microbiomesky #gutbrainaxis www.tandfonline.com/doi/full/10....

Hello world! Excited to join this new community. My name is Alex and I lead a research group at the University of Cambridge. Our primary interests are large-scale (meta-)genomic analyses of the human #microbiome, particularly in the context of health and disease.

🧬A very interesting paper on a Parkinson's disease drug reveals notable effects on iron abundance and microbiota biodiversity. Really cool experiments using ex vivo gut microbiome samples. #Science #Parkinsons #Aging #Microbiome #Research www.nature.com/articles/s41...

1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇 www.nature.com/articles/s41...

1/ Our review on sequencing-based #microbiome analysis is in the Dec 24 issue of Nature Reviews Genetics. We explore DNA/RNA-sequencing approaches for studying microbiome structure and function, highlighting the biological insights sequencing-based microbiome research offers. go.nature.com/3XFqonu

Hi Bluesky! 👋 Dipping my toes here given the dumpsterfire over at X. I am Editor in Chief of #PLOSBiology, interested in all things #science. #virologist, passionate about #OpenScience & making #publication process constructive & transparent. I look forward to rebuilding community here!

Finally took the plunge after hearing such great things

‘A place of joy’: why scientists are joining the rush to Bluesky www.nature.com/articles/d41...

Ever wondered about the story behind the cultivation of Asgard archaea? Read our new Microbe Matters by Masaru Nobu: rdcu.be/d1aEX Engineering history with Asgard archaea of the kingdom Promethearchaeati