Maliheh Mehrshad

Phage protease enzymes activate CBASS antiphage immunity https://www.biorxiv.org/content/10.64898/2026.03.04.709575v1

Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea - Nature Microbiology Uncultured open-ocean Asgard archaea can harvest light energy using rhodopsins and diverse hydroxylated carotenoid antennas.

CONGRATULATIONS galitzlil.bsky.social for receiving the Gutwirth award for the Technion best paper in 2025!!!! www.nature.com/articles/s41...

How a protein repurposes vitamin B12 as a light sensor Intense, ultrashort X-ray pulses have been used to probe the extraordinary reactions that occur in a light-sensing receptor, resolving a biochemical conundrum.

How a protein repurposes vitamin B12 as a light sensor www.nature.com/articles/d41...

🚀New study out! We identify freshwater phage-host interactions in situ using metaHi-C and connect infection dynamics with evolution.🦠

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C Detecting active phage-bacteria interactions in natural microbial communities remains a major limitation for understanding their ecological dynamics and associated co-evolutionary processes. Here, we applied metaHi-C, a chromosome conformation capture method, to resolve active virus-host associations in a freshwater microbial community. From >900 microbial and >33,000 viral Hi-C-assembled genomes, we identified 100 high-confidence phage-host linkages spanning major freshwater bacterial lineages, including Limnohabitans, Acidimicrobium, Synechococcus, Candidatus Nanopelagicus, Candidatus Planktophila, Candidatus Methylopumilus and Polynucleobacter. The inferred networks revealed diverse infection patterns, including broad-host-range phages, cellular-level co-infection, kill-the-winner dynamics and one-to-one interactions. These ecological patterns were associated with signatures of diversifying selection in host-interaction genes, consistent with host-range expansion, alongside conserved genomic regions in broad-host-range and co-infecting phages, indicating functional constraints on essential infection modules. Together, these results demonstrate that metaHi-C enables direct linking of community-level infection dynamics to underlying evolutionary processes, revealing how these forces shape bacterial population dynamics of freshwater bacteria. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 101117028 Generalitat Valenciana, https://ror.org/0097mvx21, “VIRHOS” project, Ref. CIPROM/2021/006

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C | bioRxiv https://www.biorxiv.org/content/10.64898/2026.02.18.706586v1?rss=1

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C https://www.biorxiv.org/content/10.64898/2026.02.18.706586v1

We can finally see where ecology meets evolution in phage-bacteria interactions in natural samples!

We detect diversifying selection in host-interaction genes — consistent with host-range expansion.

Yet broad-host-range phages retain conserved infection modules, suggesting functional constraints

The infection network reveal multiple ecological strategies in Freshwater phages:

• Broad host range
• One-to-one specialists
• Kill-the-winner dynamics
Annnnndddd 🥁
• Cellular level co-infection, something we are resolving in #MULTIPHAGE

From >900 microbial and >33,000 viral Hi-C genomes, we recovered 100 high-confidence phage–host links.

These span dominant freshwater taxa including:
Limnohabitans, Synechococcus, “Ca. Nanopelagicus”, “Ca. Planktophila”, Polynucleobacter & more.

#MULTIPHAGE #VIRHOS

Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard!
With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution.

Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado

www.biorxiv.org/content/10.6...

Max Fels @mfels.bsky.social from our lab discovers giant DNA viruses that infect amoeba encode eIF4E and the entire suite of 4F complex proteins to control mRNA translation, including beautiful crystal structures of viral 4E bound to modified mRNA 5' caps:

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

Protist predators engineer bacterial metabolic cooperation In the current issue of Cell Host & Microbe, Liu et al. establish a scalable framework and find that protist predation drives bacterial metabolic cooperation. This study offers insights for investigat...

Protist predators engineer bacterial metabolic cooperation

www.cell.com/cell-host-mi...

Predicting phage–host specificity - Nature Reviews Microbiology This Genome Watch article explores how protein language models are transforming phage–host specificity prediction by capturing meaningful biological information from viral sequences, from individual p...

Predicting phage–host specificity

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

So well deserved! 👏

The hidden energy cost of cellular dormancy Many organisms survive harsh environments by switching into special survival modes. Some bacteria do this by forming spores—dormant, highly resilient cells that can persist for years or even centuries...

www.growkudos.com/publications...

New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org

Mapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events ...

🌊Paper announcement! 📣
Viral infections rewire the metabolic makeup of their host and thereby create distinct chemical signatures. Can we use metabolic biomarkers to diagnose infections of algal blooms in the ocean?
Well, take a look at our new article led by Conny Kuhlisch in @pnas.org
>>

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...

New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.

We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.

www.biorxiv.org/content/10.6...

Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?

Then come and join our group !

A prophage-expressed type IV pilus component provides anti-phage defense Sztanko et al. demonstrate that Pseudomonas aeruginosa prophages encode proteins resembling the type IV pilus minor pilin protein, FimU. These prophage-expressed FimU proteins are incorporated into th...

Anti-phage defense through prophage-exprrssed type IV pilus

www.cell.com/cell-reports...

Comprehensive hallmark gene sequence, genomic and structural analysis of Picornavirales viruses clarifies new and existing taxa https://www.biorxiv.org/content/10.64898/2026.01.05.697625v1

Postdoc - Microbiome - Innovative Genomics Institute University of California, Berkeley is hiring. Apply now!

🚨 Our Lab is HIRING! If you are interested in characterizing model microbiomes using genome-resolved methods, statistical/metabolic modeling, and/or machine learning please submit an application here: aprecruit.berkeley.edu/JPF05234

#postdoc #sciencejobs #biology #microbiome

The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky

Why would anyone want to be a scientist? It is difficult to fathom why anyone intelligent enough to be a scientist would actually choose to be one. Doing good science requires the utmost exertion of body, mind and spirit, yet is consistently...

A lovely read!

Why would anyone want to be a scientist!?

journals.biologists.com/jcs/article/...

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...

Finally, we’ve solved a long-standing mystery: what tintinnid shells are actually made of:
A new class of biomaterial formed by remarkable structural proteins unique to tintinnids.
A major milestone after 3 years of work! Read about it in our preprint: doi.org/10.64898/202...
#ProtistsOnSky

All you want for christmas is.... transposon mutagenesis!

Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.

Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

Microbial rhodopsins are everywhere in the surface ocean, but were assumed to play a role mainly when nutrients are scarce. Our new study reveals unexpected rhodopsin dynamics tightly linked to phytoplankton blooms.

The glycine betaine-cobalamin feedback loop drives cross-feeding between marine bacteria and algae https://www.biorxiv.org/content/10.64898/2025.12.19.695462v1