Vivek Mutalik
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vivekmutalik.bsky.social
Vivek Mutalik
@vivekmutalik.bsky.social
Dad, Teacher, Artist, Gardener and Scientist.

Change is permanent. This moment will pass. It has to.

Ps.
All I post is my personal opinion, in my personal times, using my personal tools, not my employers.
Pinned
📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
Phage Foundry
phagefoundry.org
Reposted by Vivek Mutalik
Excited to share our new study! Great fun working again with my good friend @stephenrgarrett.bsky.social — always a highlight! Huge thanks to fantastic co-authors @samkaytucker.bsky.social, @drandyjroe.bsky.social and our star technician Vojtech Pavelka. academic.oup.com/nargab/artic...
November 21, 2025 at 6:27 PM
Reposted by Vivek Mutalik
I started studying phages just over 4 years ago. The project that started it all is finally published. We isolated 6 closely related anti-Acinetobacter phages and showed that they are not capsule-specific and can reduce bacterial load in a rat model. More work still to come on this! #phagesky #IDsky
A bacteriophage genus infects carbapenem resistant Acinetobacter baumannii via a non-capsular receptor and provides protection in vivo
Microbiology; Virology
www.cell.com
November 22, 2025 at 1:11 PM
Thrilled to share our new work uncovering how membrane transporters determine resource-size preferences in gut bacteria, and showing that deleting a single protein domain can shift a transporter’s preference from long to short fructans. www.biorxiv.org/content/10.1...
Niche partitioning by resource size in the gut microbiome
Niche partitioning promotes diversity of the human gut microbiota. However, the molecular basis of resource specialization and niche separation in the gut remains poorly understood. Here we show that ...
www.biorxiv.org
November 23, 2025 at 8:13 AM
Reposted by Vivek Mutalik
#NatMicroPicks

Drug-delivering bacteria for Parkinson's! 🦠🧠

A genetically engineered E. coli delivers L-DOPA improving motor and mood outcomes in Parkinson’s models

#MicroSky #SynBio

www.sciencedirect.com/science/arti...
Bioengineered gut bacterium synthesizing levodopa alleviates motor deficits in models of Parkinson’s disease
L-3,4-Dihydroxyphenylalanine (L-DOPA), synthesized from L-tyrosine, is a direct precursor to dopamine. L-DOPA is the gold-standard treatment for Parki…
www.sciencedirect.com
November 20, 2025 at 5:13 PM
Reposted by Vivek Mutalik
New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
Reposted by Vivek Mutalik
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org
November 19, 2025 at 6:35 PM
Reposted by Vivek Mutalik
Congratulations to my student Josh Hensley and our amazing collaborators at UCSD David Pride lab! In press today, we developed a technique to evolve phages to broaden bacterial host range to tackle bacteria that evade antibiotics. #phagesky #phage #microsky #virussky

www.nature.com/articles/s41...
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates - Nature Communications
Ghatbale et al. adapted a co-evolutionary technique to develop Klebsiella pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates, including drug resistant isolate...
www.nature.com
November 19, 2025 at 4:47 PM
Reposted by Vivek Mutalik
Our lab from @HHMINEWS & @UCBerkeley is looking for undergrads to come for an internship!
www.hhmi.org/programs/cec...
Summer Undergraduate Research Experience | HHMI
The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.
www.hhmi.org
November 20, 2025 at 1:59 AM
Hmmm
This work has so many implications on literature 😳😬

Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS
Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular reactive oxygen species (ROS) in innumerable studies. Their...
www.pnas.org
November 19, 2025 at 5:03 AM
Reposted by Vivek Mutalik
Interested? Read the pre-print, or check out our code ⬇️

Preprint: www.biorxiv.org/content/10.1...
GitHub repo: github.com/Noonanav/Gen...
www.biorxiv.org
November 16, 2025 at 11:16 PM
Reposted by Vivek Mutalik
OUR APPROACH: Interpretable genomic features + ML to predict interactions. Phylogeny-agnostic feature construction so it works for novel phages and bacteria. We trained and tested across 5 public datasets (128,357 interactions total) and validated with high-throughput phenotyping + RB-TnSeq.
November 16, 2025 at 11:16 PM
Reposted by Vivek Mutalik
THE CHALLENGE: Bacteria and phages are incredibly diverse. Experimentally testing each phage against a new bacterial target isn't feasible. But finding the right phage quickly could be life-saving, especially for drug-resistant infections where treatment options are limited.
November 16, 2025 at 11:16 PM
🎉🎊🙌 😎
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.

www.biorxiv.org/content/10.1...
www.biorxiv.org
November 17, 2025 at 12:15 AM
Reposted by Vivek Mutalik
Interesting CRISPRi screening in Smeg to identify factors modulating resistance to antimicrobials (new insights into the role of the cell envelope)
November 16, 2025 at 1:41 PM