Jerónimo Rodríguez-Beltrán

Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strain...

Hey y’all,

New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae

www.microbiologyresearch.org/content/jour...

Frontiers | Genome assembly and functional predation analysis of novel Bdellovibrio isolates from human gut microbiota IntroductionPredatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ec...

🧬New paper out! We report the first isolation of viable B. bacteriovorus predators from human gut microbiota. www.frontiersin.org/journals/mic.... Great work of Mario Romero @migueldiezfdz.bsky.social @josete600.bsky.social and @rosacampo.bsky.social

Pictured is a map of plasmids, which are DNA molecules that can be transferred between bacteria. Each ring and dot represents an evolved plasmid and a mutation, respectively. Image credit: Paula Ramiro-Martínez.

In this issue: Fresh light on horse evolution, mangrove restoration as coastal flood protection, and the links between aerobic metabolism and planetary oxygenation. In PNAS: https://ow.ly/yB6J50Y5ykK

And what a beautiful @pnas.org cover @paularamiro.bsky.social and @jerorb.bsky.social !!!!!! You should be very proud!

Thank you!!

Thank you, Carmen!

Thank you, Vaughn! It’s usually tough to compete with all the cute animal covers they usually pick, so I’m really proud this one got chosen!

Thank you!

New paper out in @pnas.org, and it made the cover! 👁️

We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.

‼️Check Paula’s 🧵 and the paper👇

𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

Our new paper on Insertion Sequences (IS) in #Klebsiella

- Lineages have vastly different IS loads and profiles
- An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution.

www.microbiologyresearch.org/content/jour...

New preprint from the lab!

Stress-Induced Cooperation Promotes Tolerance in Resource-Limited Auxotrophic Microbial Consortia.

Great and long journey with great collaborators.

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

Coupling DNA processing to early gene expression drives antibiotic resistance plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.01.09.698686v1

Microbial Evolution: Impacts on Human Health Call for Papers A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases. This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution. Submission – open until January 31, 2027 Guest editors Robert Woods, MD PhD, University of Michigan Camilo Barbosa, PhD, University of Michigan Silvie Huijben, PhD, Arizona State University

🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health

Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me

This will be great, please submit and share!
academic.oup.com/emph/pages/m...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics Mobile genetic elements (MGEs), including plasmids and viruses, drive microbial evolution and ecosystem dynamics, yet their distribution, host range, and functions remain poorly understood, especially...

New preprint out: Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics
www.biorxiv.org/content/10.6...

@mingyan-igi.bsky.social

I guess science Santa gave you coal…🧑‍🎄 🪨

🎁 Getting a paper acceptance right before Christmas break is one of the best feelings. 100% recommend.

Happy holidays, everyone! 🎄✨

Congrats, Chris! Very well deserved!!

Genomic Flexibility Through Extrachromosomal Amplifications: A Leishmania Survival Strategy https://www.biorxiv.org/content/10.64898/2025.12.13.692850v1

Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...

Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...

Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...

My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)

Genome Biology and Evolution | December 2025 cover

The December cover of Genome Biology and Evolution features Rojas-Triana et al., who publish a Review on the adaptive potential of extrachromosomal circular DNA across taxa.

🔗 doi.org/10.1093/gbe/evaf223

#genome #evolution

Collateral sensitivity and genetic vulnerability of antibiotic resistance

An unprecedented DNA recognition–mimicry switch governs induction in arbitrium phages Temperate phages integrate multiple information sources to regulate lysis-lysogeny transitions. SPBeta-like phages use arbitrium signalling and DNA damage to control repressor activity during lytic in...

Excited to share our latest work with @albertomarina.bsky.social and @avigdoreldar.bsky.social labs, where we decipher the mechanism by which SPβ-like phages sense the SOS response to control the lysis–lysogeny switch. www.biorxiv.org/content/10.1...

On the plane after a fantastic few days in Liverpool at #MicroEvo25 organised by the @microbiologysociety.org. The science, the people, and the city were all way above expectations. I’m definitely coming back. Had an absolute blast!

What a week! Thanks to everyone who attended the UK Phage Therapy workshop and #MicroEvo25 in Liverpool… every talk, poster, question, chat, and round of applause helps to build our microbial evolution community! Thanks to @microbiologysociety.org and @ukri.org for support

What is the best strategy to win any contest?

Eliminate your opponents of course.

Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.

www.biorxiv.org/content/10.1...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...