Alexandre Almeida
@alexmsalmeida.bsky.social
MRC Career Development Award fellow at the University of Cambridge | Group Leader of the Microbiome Function and Diversity lab (https://microfundiv-lab.github.io) | Bioinformatics, Machine Learning, Metagenomics, Functional modelling, Human microbiome
Pinned
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...
www.nature.com
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
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.
Feel free to reach out with a CV and cover letter stating your interest in this project.
October 15, 2025 at 3:37 PM
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.
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
Apply here: forms.office.com/e/sdys5HATUH
October 14, 2025 at 3:07 PM
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
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...
Further info: www.giba-uk.org/training-opp...
Apply here: forms.office.com/Pages/Respon...
Home | Giba Network UK | Gut Immune Brain Axis Network
Gut Immune Brain Axis Network (GIBA Network)
www.giba-uk.org
October 1, 2025 at 2:45 PM
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...
Further info: www.giba-uk.org/training-opp...
Apply here: forms.office.com/Pages/Respon...
Reposted by Alexandre Almeida
📊 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...
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...
October 1, 2025 at 8:38 AM
📊 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...
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...
Reposted by Alexandre Almeida
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
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
September 22, 2025 at 10:44 AM
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
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
Reposted by Alexandre Almeida
✔️ 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
✔️ 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
September 22, 2025 at 12:51 PM
✔️ 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
✔️ 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
Reposted by Alexandre Almeida
“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...
@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...
September 22, 2025 at 10:56 AM
“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...
@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
September 22, 2025 at 12:16 PM
Representing the bioinformatics crowd at the #GIBANetworklaunch
Reposted by Alexandre Almeida
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
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
September 22, 2025 at 9:42 AM
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
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...
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...
www.biorxiv.org
September 10, 2025 at 11:44 AM
🚨 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...
July 14, 2025 at 2:27 PM
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...
Reposted by Alexandre Almeida
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...
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...
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
www.bio.cam.ac.uk
April 28, 2025 at 12:16 PM
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...
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...
Reposted by Alexandre Almeida
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
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
www.bio.cam.ac.uk
April 28, 2025 at 11:34 AM
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
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
www.bio.cam.ac.uk
April 28, 2025 at 9:33 AM
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
Reposted by Alexandre Almeida
argNorm is published now academic.oup.com/bioinformati...
April 17, 2025 at 4:57 AM
argNorm is published now academic.oup.com/bioinformati...
Reposted by Alexandre Almeida
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...
A great summary of the state of the art for microbiome research.
www.nature.com/articles/s41...
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.
www.nature.com
April 11, 2025 at 2:51 PM
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...
A great summary of the state of the art for microbiome research.
www.nature.com/articles/s41...
Reposted by Alexandre Almeida
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...
🔗 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
www.nature.com
April 9, 2025 at 6:04 AM
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...
🔗 www.nature.com/articles/s41...
Reposted by Alexandre Almeida
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...
If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
March 27, 2025 at 4:34 AM
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...
If so, you might this little project: github.com/rrwick/conda...
Reposted by Alexandre Almeida
New to bluesky - would appreciate a "retweet" please, so I can find everyone from twitter.
February 26, 2025 at 11:36 AM
New to bluesky - would appreciate a "retweet" please, so I can find everyone from twitter.
Reposted by Alexandre Almeida
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
These findings from @alexmsalmeida.bsky.social et al. highlight the critical role of the intestinal milieu in the colonization success of opportunistic pathogens
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.
www.nature.com
January 23, 2025 at 10:43 AM
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
These findings from @alexmsalmeida.bsky.social et al. highlight the critical role of the intestinal milieu in the colonization success of opportunistic pathogens
Reposted by Alexandre Almeida
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/...
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/...
January 24, 2025 at 2:50 AM
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/...
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/...
Reposted by Alexandre Almeida
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...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
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...
www.cell.com
January 23, 2025 at 4:12 PM
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...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Reposted by Alexandre Almeida
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!
• 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!
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 …
microbiomedigest.com
January 17, 2025 at 7:57 AM
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!
• 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!
Reposted by Alexandre Almeida
🆕 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
https://buff.ly/40gVxNH
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.
quadram.ac.uk
January 17, 2025 at 9:07 AM
🆕 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
https://buff.ly/40gVxNH
Reposted by Alexandre Almeida
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 🧪
January 15, 2025 at 1:23 PM
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 🧪