Alexandre Almeida

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

Thanks Florian! That's very cool. Would be great to connect at some point. We would be very interested in following this up and explore potential collaboration opportunities.

Really excited about this work, showing how the understudied portion of the microbiome may have important clinical relevance.

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health The human gut microbiome plays an important biological role in host health, yet over 60% of gut species remain uncultured and hence inaccessible to experimental manipulation. Here we analysed 11,115 h...

🚨 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...

Cambridge partners on a new UK research network to unlock A groundbreaking UK research network has been launched by UKRI to uncover how gut health influences the brain, immune system, and mental well-being – potentially leading to new treatments for

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.🧠👇🏽

Working with Jon Swann, Jessica Teeling,
@parker-aim.bsky.social and
@denklab.bsky.social we will be bringing together everyone across the UK interested in any facet of the GIBA (academia, industry, public). Do register your interest here: www.giba-uk.org

Cambridge partners on a new UK research network to unlock A groundbreaking UK research network has been launched by UKRI to uncover how gut health influences the brain, immune system, and mental well-being – potentially leading to new treatments for

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...

Clinical translation of microbiome research - Nature Medicine This Review summarizes recent and compelling examples of microbiome-based interventions that are ripe for clinical adoption while also discussing the challenges and opportunities facing the field.

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...

Exploring the causal role of the human gut microbiome in endometrial cancer: a Mendelian randomization approach - Scientific Reports Scientific Reports - Exploring the causal role of the human gut microbiome in endometrial cancer: a Mendelian randomization approach

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...

GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

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.

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 Enterobacteriaceae in terms of functional pathways and metabolites in healthy human gut microbiomes.

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/...

Structure-guided discovery of viral proteins that inhibit host immunity Large-scale, structure-guided computational pipeline sifts through millions of phage proteins to identify those that bind and antagonize host immune proteins. Detected proteins are shown to inhibit no...

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...

January 17, 2025 Starting the new year with a new digest out, full of interesting findings.Check it out and see you at MVIF next week! Human gut microbiome Early life microbial succession in the gut follows common …

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!

Is there a “brain microbiome”? No - Quadram Institute There is no scientific evidence of a brain microbiome, including no imaging, DNA-sequence-based or culture-based or immunological evidence.

🆕 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

This is figure 2, which shows the distribution and diversity of the most prevalent Enterobacteriaceae species.

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 🧪

Thanks Ana. Look forward to working together on many more exciting projects!

🎉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