Rodrigo Sánchez Martínez

Illuminating the newly produced viruses within the virosphere with BONCAT and single virus genomic sequencing technologies academic.oup.com/ismecommun/a... #jcampubs

Unraveling posttranscriptional regulatory networks in phage infection Phages employ sophisticated transcriptional regulatory networks to optimize replication. Recently, Silverman et al. used RIL-seq (RNA interaction by l…

Like bacteria, phages use sRNAs to regulate gene expression! Out today in @cp-trendsmicrobiol.bsky.social, @mvelascogomariz.bsky.social and I highlight a recent RIL-seq study from the @saharmelamed.bsky.social lab that looked into posttranscriptional regulation of lambda!

tinyurl.com/lambda-RIL-seq

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...

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

Boosting origin of life theory, RNA comes close to copying itself Some RNA molecules can create their own mirror images, suggesting similar molecules could have sparked life

Researchers report creating RNAs that can generate a sort of mirror image of themselves and use that template to generate the original.

Learn more: https://scim.ag/46F2BHN

Muchas gracias Miguel! Un abrazo 🤗❤️

Thanks for the support, Mart. Never give up!!😊

Gracias Esteban! Un abrazo fuerte ❤️

Double Marie Curie win! My lab and life partner, @alopezm.bsky.social, and I have both been awarded MSCA Fellowships with @baerboletta.bsky.social. Exciting times ahead! 🚀

A figure from the paper that provides an overview of available culture-dependent and culture-independent approaches for characterizing the human gut virome. Both culture-dependent and culture-independent approaches should be used to study the gut virome. At the bench, many protocols have been adapted to enrich viruses in a sample and isolate them using a sensitive host. Once a virus is isolated, various assays can be used to characterize how the virus interacts with its bacterial host. On the command line, viral genomes can be predicted and viral taxonomy can be identified within a sample. Once procured, multiple tools can be used to annotate viral genomes for predicted gene content and viral lifestyle and predict bacterial host taxonomy.

It's increasingly clear that commensal viruses play important roles in human health, but how do you study them?

Our review "Tools and approaches to study the human gut virome: from the bench to bioinformatics" is out today in mSystems! journals.asm.org/doi/10.1128/...

@haleybiont.bsky.social

mvif 46 program

It's Friday!
...and a new #MVIF program is out! 🤩

Free registration: cassyni.com/s/mvif-46

Highlights:
🇺🇸 Rebecca L. Knoll
🇯🇵 Akito Sakanaka

Keynote:
🇺🇸 @simrouxvirus.bsky.social

⭐️ Talks:
🇦🇺 @jeremyjbarr.bsky.social
🇨🇦 @erikbakkeren.bsky.social
🇨🇳 Guanxiang Liang

A phage protein screen identifies triggers of the bacterial innate immune system - Nature Microbiology A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...

Ecological ubiquity and phylogeny drive nestedness in phages–bacteria networks and shape the bacterial defensome Author summary Viruses that infect bacteria, known as phages, are part of microbial communities and influence the abundance, diversity, and traits of their hosts. In an agriculture-related context, th...

#microsky #phagesky #phage
At last! Great to see this one out: journals.plos.org/plospathogen...

Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social

Happy to share our recent preprint:
"DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity"

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

@spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social

Two fantastic papers published back-to-back in @natmicrobiol.nature.com show that strictly lytic phages can persist intracellularly for long periods of time. Very much in line with ideas we had suggested in a recent study. Highly recommended reads 👇
www.nature.com/articles/s41...

Check the consensus level of different techniques used to unveil the viral diversity from nature in our latest paper

link.springer.com/article/10.1...

Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it Abstract. An unbiased and accurate estimation of intraspecies diversity, i.e., the extent of genetic diversity within species (or microdiversity), is cruci

Happy to share our latest paper focused on the effect of uneven sequencing depth in intraspecies diversity estimates (nucleotide diversity and ANIr) using environmental and synthetic metagenomes

academic.oup.com/ismecommun/a...

Context-Dependent Metabolic Adaptation in Microbial Communities: From Monocultures to Complex Ecological Interactions https://www.biorxiv.org/content/10.1101/2025.10.22.683057v1

Happy World Phage Week to All Who Celebrate Microbes get sick too - infected by bacteriophage or simply ‘phage’. A first post in a series on the hidden world of phage & how they transform human and environmental health.

In a break from recent themes & in honor of World Phage Week (Oct 22-28), some reflections on the world of bacteria and phage, part of a short series explaining the rationale for why we have invested so much time in exploring when microbes get sick too.

joshuasweitz.substack.com/p/happy-worl...

Amazing work Yifan, congrats!! 👏🏼

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

How exercise promotes the immune system vs cancer, working through a gut bacteria metabolite
www.cell.com/cell/abstrac...

“Treatment with bacteriophages can combat antibiotic-resistant infections, but Swiss patients lack access” It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in th...

It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in therapy. What would need to change? Researcher Alexander Harms explains.

ethz.ch/en/news-and-...

Deep-mining the archaeal proteome for antibiotics - Nature Microbiology A deep-learning algorithm unravels a collection of archaeasins, peptides from the archaeal proteome with potential antimicrobial activity and implications for the development of next-generation antibiotics

Excited to highlight our News & Views on the article by Torres et al. from @delafuentelab.bsky.social team 🚀 Archaea could help to discover new antibiotics!

Read it here:
www.nature.com/articles/s41...

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.

Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.

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

Deep-mining the archaeal proteome for antibiotics Nature Microbiology - A deep-learning algorithm unravels a collection of archaeasins, peptides from the archaeal proteome with potential antimicrobial activity and implications for the development...

Deep-mining the archaeal proteome for antibiotics

News & Views by Rafael Laso-Pérez

@gecko1990.bsky.social @delafuentelab.bsky.social

Read it here: rdcu.be/eHNwa

Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them Abstract. The importance of rarefying ecological or amplicon sequencing data to a standardized level of diversity coverage for reliable diversity compariso

Excellent work done by Borja, Miguel, and Kostas!

Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them

academic.oup.com/ismecommun/a...

A new work on how context matters... from the PhD Thesis of Rodrigo the Great

Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils Abstract. Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determ

Happy to share our upcoming paper on pioneer microbial communities, including viruses, establishing after glacier retreat, result of a great collaboration @ua.es @mncn-csic.bsky.social @univgirona.bsky.social @pepa-anton.bsky.social @estherrubioport.bsky.social academic.oup.com/ismecommun/a...