Sambhawa Priya

Resharing the thread on our recent paper exploring how HIV and antiretrovirals shape the gut microbiome across global cohorts 👇

It was an absolute pleasure working together with the brilliant first author, Dr. Karolina Sjöberg Jabbar, and the entire team during my postdoctoral work in the Xavier lab at the Broad Institute. Grateful to see this work out in the world!

Antiretrovirals also shaped gut ecology. In Uganda & Botswana, efavirenz was linked to Prevotella loss. Computational & in vitro experiments showed that efavirenz may inhibit bacterial reverse transcriptases involved in antiphage defense, disrupting non-Western Prevotella-rich ecosystems.

Although taxa varied by region, shifts in microbial functions were shared across HIV cohorts: reduced carbohydrate-utilization and motility/sporulation genes, and enriched mannose PTS transporters—pointing to a shift toward mucosal colonizers in an inflamed gut.

At taxonomic level, we observed both geography-specific shifts (e.g. Uganda→Botswana→US gradient in Prevotella) as well as shared alterations (e.g. depletion of Faecalibacterium prausnitzii across cohorts with HIV), which also helped predict HIV status across sites.

Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes - Nature Microbiology Metagenomic analysis of the gut microbiome of people with human immunodeficiency virus (HIV), from three distinct cohorts, revealed infection- and antiretroviral drug-linked alterations, which may con...

A bit late to share this, but excited about our new Nature Microbiology paper on how HIV and its therapies shape the gut microbiome! Using metagenomes from Uganda, Botswana, and the US, we map gut microbiome shifts linking HIV, treatment & host health 🧵

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

🧬 🦠 🏙️
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?

Excited to share our new paper: www.biorxiv.org/content/10.1...

Proud of the latest edition of my free intro biostats book.

gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/

Not complete but at a good point to take a break, and I think its quite usable

dm me with comments , ideas etc

Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...

Thinking about a postdoc in microbiome science?
Our lab at the MPI for Biology (Tübingen) builds on the culture I established at Cornell: collaborative, creative, and internationally diverse. Postdocs lead their own projects with secure funding. Join us!
#PostdocJobs #HostMicrobe #AcademicJobs

Genomics of host–microbiome interactions in humans Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...

For #worldmicrobiomeday, re-sharing our recent Review by @pamferretti.bsky.social, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social on the 'Genomics of host–microbiome interactions in humans', which is free to read using this link: rdcu.be/etIRy

Genomics of host–microbiome interactions in humans Nature Reviews Genetics, Published online: 04 June 2025; doi:10.1038/s41576-025-00849-8In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

ICYMI: New online! Genomics of host–microbiome interactions in humans

Genomics of host–microbiome interactions in humans - Nature Reviews Genetics In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

Just out in Nature Reviews Genetics!

From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome!

Fun working together with
@pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson

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

📣 Happy to share our review on host-microbiome genomics!

We synthesize the growing field exploring interactions between human genetics and the microbiome, building a roadmap for mapping the dialogue between our genes and microbes

Out now in Nature Reviews Genetics👇

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

Genomics of host–microbiome interactions in humans Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...

Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field.
rdcu.be/epoRR

@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.

The R Graph Gallery – Help and inspiration for R charts The R graph gallery displays hundreds of charts made with R, always providing the reproducible code.

Ever stuck choosing the right plot or trying to figure out how to make it look just right? My go-to resource is the R Graph Gallery (r-graph-gallery.com), which is full of examples and clear code for everything from scatterplots to Sankey diagrams! #dataviz #rstats #rladies

The eternal question: should you focus on one problem for a very long time or is it more productive to bounce and work on many problems? David Baker says that both modes have been important in his career trajectory.
podcasts.apple.com/us/podcast/n... @nightsciencepod.bsky.social

These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today.

We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe

www.cell.com/cell/current...

Check out Samantha's thread for a deep dive into the results 👇

bsky.app/profile/sama...

Integration of 168,000 samples reveals global patterns of the human gut microbiome The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

Today we report a new compendium of human gut microbiomes with >168,000 samples

By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria

Now out in Cell:

www.cell.com/cell/fulltex...