Sahar Melamed

Bacteriophage-Encoded Small RNAs: Emerging Tools for Phage Therapy and Antibacterial Intervention - Aviezer Silverman, Sahar Melamed, 2026 Bacteriophages (phages) are viruses that specifically infect bacteria and play a central role in shaping microbial communities and bacterial evolution. Beyond t...

🚨Happy to share our new mini-review on phage-encoded small RNAs and their potential for phage therapy and antibacterial strategies, written with Aviezer Silverman!
journals.sagepub.com/doi/10.1177/...
#RNA
#phage
@journals.sagepub.com
@hebrewuniversity.bsky.social
@phagedirectory.bsky.social

tRNA gene arrays: emerging roles in bacterial persistence and adaptive evolution Bacterial tRNA genes often form arrays that are thought to enhance translational efficiency. Recent work shows that tRNA gene arrays also regulate persistence in Burkholderia, correlating with phylogenetic relationships. These findings implicate tRNA gene arrays in niche-specific adaptive evolution, extending bacterial persistence beyond survival under lethal stresses.

tRNA gene arrays: emerging roles in bacterial persistence and adaptive evolution

Well deserved choice!

mGem: Horses for courses in mapping bacterial small RNA interaction networks | mBio Small RNAs (sRNAs) are bacterial RNA species that are anywhere between 50 and 500 nucleotides in length. Many sRNAs employ a short sequence (as few as 6 nucleotides), known as the seed sequence, to ba...

I never expected horses 🐎 in my RNA research, but here we are 😁
In our new perspective, Simon Dove and I discuss how RIL-seq maps transcriptome-wide sRNA networks in vivo and how iRIL-seq expands the RNA–RNA interaction toolbox.
journals.asm.org/doi/10.1128/...
@hebrewuniversity.bsky.social

Proud to see our work featured in this Spotlight in @cp-trendsmicrobiol.bsky.social by @mvelascogomariz.bsky.social and @jenshoer.bsky.social!
They highlight how phage infection involves surprisingly rich posttranscriptional regulatory networks and sRNA-based regulation.
Thank you for the spotlight!

Last week we started the day with a lab hike and breakfast in the beautiful mountains around our faculty. Team bonding before getting back to science!
#RNA
@hebrewuniversity.bsky.social

Warm wishes for the new year from the Melamed lab! I am happy to work with such a great team. Wishing you curiosity, progress, and shared success.

Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.

#microsky #phagesky #phage

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

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings re...

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle: Molecular Cell www.cell.com/molecular-ce...

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings reveal a previously unrecognized RNA-level regulatory layer in phage-host interactions and highlight the role of post-transcriptional control in promoting phage infection.

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

Thanks Chuan!

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings re...

Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...

Happy Hanukah and happy holiday season from the Melamed lab!

Congratulations Chuan! Cool work

How does a bacterial small RNA evolve new functions?

Our new study reveals the stepwise evolutionary journey of UhpU, a 3′UTR-derived sRNA in E. coli and relatives. It evolved from a metabolically-focused regulator to one with expanded targets and biogenesis manner.

www.pnas.org/doi/10.1073/...

Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh

KlebPhaCol paper is now out! Go check it out and see all that we offer.

And when ready, visit our website for more: www.klebphacol.org

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

An RNA sponge directs the transition from feast to famine in Caulobacter crescentus - Nature Communications In bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone Hfq to modulate gene expression at the post-transcriptional level. Here, the authors identify global Hfq-mediated RNA-R...

Cool work by @microberna.bsky.social & Kai Papenfort, presenting the first RNA-RNA map in C. crescentus using RIL-seq, revealing an RNA sponge that controls the transition from nutrient abundance to starvation; new insights into RNA networks and stress responses!
#RNA
www.nature.com/articles/s41...

History of Phage Therapy — ThePhageCollectionProject Phage therapy is not a recent discovery; it dates back to the early 20th century, with two scientists making impactful discoveries within two years of each other. But research priorities shifted towar...

🔬 To celebrate World Phage Week, this month's issue of the Phage Collection Blog, written by Hana, explores the history of phage therapy. Thanks to @danielarothschild.bsky.social for providing the cover image, showcasing phage ROTH78.

#WorldPhageWeek

www.phage-collection.org/blog/history...

‘Nightmare bacteria’ cases are increasing in the U.S. It’s likely that many people are unrecognized carriers of the drug-resistant bacteria, which could lead to community spread, CDC scientists said.

CDC reports that the 'nightmare bacteria' with the NDM gene infections rose ~ 70% from 2019–2023 & is resistant to almost all antibiotics.

At GARDP, Shionogi’s approved antibiotic cefiderocol & Bugworks’ BWC0977, now in clinical development, show activity against it.

🔗Read: bit.ly/4pFG05H

Call for Applications for the Azrieli International Visiting PhD Fellowship - The Azrieli Foundation The Azrieli International Visiting PhD Fellowship offers outstanding international PhD candidates the opportunity to conduct short-term research in Israel, fostering academic collaboration and strengt...

PhD students! Curious about RNA biology, phages & interbacterial interactions? Come spend 3–4 months in my lab through the Azrieli International Visiting PhD Fellowship (ILS 12K/month). Collaborate and experience science & culture together!
azrielifoundation.org/azrieli-fell...

Wonderful department retreat yesterday! Proud of Hila Robard’s excellent talk about Pseudomonas aeruginosa small RNAs and their physiological impacts!
Big thanks for the organizers Gideon Mamou and Yiska Weisblum!

The Melamed and Altuvia labs are on their way to the Meeting on Regulating with RNA in Bacteria and Archaea in #Strasbourg !!! Excited meet old friends and make new ones
#RNA

Uncovering phenotypic inheritance from single cells with Microcolony-seq Microcolony-seq systematically uncovers inherited phenotypic diversity directly from infected human samples, revealing that bacteria can retain long-term genetic and nongenetic memory from the host en...

A new cool method developed by the Balaban lab, Microcolony-seq.
A new way to track bacterial phenotypic inheritance, revealing hidden subpopulations in infections.

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

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa Abstract. Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and di

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa 🦠👏High-throughput tRNA epitranscriptome profiling using mass spec on P. aeruginosa transposon insertion library and links with metabolic networks #microsky #rnasky doi.org/10.1093/nar/...

Microbial metal physiology: ions to ecosystems Nature Reviews Microbiology, Published online: 25 July 2025; doi:10.1038/s41579-025-01213-7Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review, Helmann discusses the key chemical concepts underlying microbial metal physiology and highlights several exemplary microbial systems.

New online! Microbial metal physiology: ions to ecosystems

I enjoyed attending the annual Israel Society for Microbiology (ISM) meeting. This year held special significance in honoring the memory of two esteemed faculty members, Prof. Herve Bercovier and Prof. Hanna Engelberg-Kulka, who sadly passed away over the past year.

This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Phage tRNAs: decoding the enigma The presence of tRNAs in bacteriophage genomes has intrigued scientists since their discovery in the early 1960s, as phages were believed to rely on the host tRNAs for their translation. Over the years, a multitude of hypotheses have been explored, providing evidence that phages with different lifestyles utilize tRNAs in distinct ways. In recent years, several studies have provided evidence that phage tRNAs play a crucial role in evading phage defense systems. In this review we summarize the current state of the field of phage tRNAs, highlighting their diverse roles in phage infection. We also discuss the host response to phage tRNAs and the application of this knowledge to improve phage-based therapeutics to combat bacterial infections.

Phage tRNAs: decoding the enigma