Cathy Hernandez
@cathyhernandez.bsky.social
Assistant Professor at the University of South Carolina | bacteria x (pro)phage x environment | hdzlab.com
EEB Mentor Match is now open! But apps due soon (8/17). Mentees: get help applying for grad school or fellowships in ecology & evolution. Mentors: senior grads, post-docs, or faculty in these fields willing to give advice Org by Diversity Cmte of @asn-amnat.bsky.social Pls share! eebmentormatch.com
EEB Mentor Match
Visit the post for more.
eebmentormatch.com
Out Now! Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils #MicroSky
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils
Nature Microbiology, Published online: 29 June 2026; doi:10.1038/s41564-026-02391-7An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.
go.nature.com
We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/
SOS-mediated prophage induction constrains resistance evolution to DNA-damaging antibiotics
Most naturally occurring bacteria are lysogens, encoding one or more temperate phages (prophages) integrated into their genome. As prophages are induced by the bacterial SOS response, DNA-damaging ant...
biorxiv.org
The list of Ecology/Evolution/Marine Bio Labs recruiting grad students for Fall 2027 is live! PIs enter your position info here: forms.gle/MAGd4ohyPeoY... students (and PIs not recruiting) share the composite list: docs.google.com/spreadsheets... Please share widely! 🧪
Ecology/Evolution/Marine Biology labs recruiting for Fall 2027
Please complete this form if you are a PI recruiting graduate students for a Fall 2027 start. If you are NOT recruiting, feel free to share the response sheet with prospective students looking for lab...
forms.gle
Come by my poster (AEM 737) today from 3-4PM if you’re interested in phage therapy, Pseudomonas lung infections, phage training, or filamentous phages!
Paul Turner Lab@paulturnerlab.bsky.social · 2mo agoTurner Lab Graduate Student @noahhoupt.bsky.social is giving a poster today on how genetic diversity in chronic P. aeruginosa infections poses challenges for phage therapy. Check out his poster in the AEM area (#737 at 3-4PM).
Last day of #ASMicrobe, with a lot of exciting talks and sessions still to come ! Including one near and dear to my heart: long-term dynamics of environmental microbiomes, where we'll hear all about time-series 'omics datasets across many ecosystems, from rivers to soils to insects (and more) 🎉
Research Scientist from our lab @antanij.bsky.social presenting TODAY at 10.45 am in the Mechanism Discovery Hub (area near posters in the exhibit halls). #ASMicrobe
Jyot Antani@antanij.bsky.social · 3mo agoLooking forward to presenting at ASM Microbe 2026! @asm.org Grateful for the opportunity to share our work and learn from so many brilliant researchers in one place. See you in Washington, D.C. #ASMicrobe invt.io/1bxbe1gvcjt
Come see my former postdoc @cathyhernandez.bsky.social’s presentation on how prophages shape thermal performance in marine bacteria (room 147AB at 12:15PM). Cathy is now a professor at the University of South Carolina and is recruiting PhD students for Fall 2027!
Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
nature.com
Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...
Ecology and evolution of host-parasite interactions in a changing world | CNRS - Conférences Jacques Monod (CJM)
cjm.sb-roscoff.fr
Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky
PhiSpyWeb – Browser-based Prophage Prediction
Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly
linsalrob.github.io
When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So @brownlab.bsky.social and I wrote this, and I'm happy to share the preprint!
The bacterial immune system: identifying evolved defense adaptations
ecoevorxiv.org
New book "A Primer for Experimental Evolution" with coauthors Michael Rose, Margarida Matos, and Joe Graves. www.worldscientific.com/worldscibook... A compact primer for students and colleagues interested in planning and designing experiments to address questions in evolutionary biology.
A Primer for Experimental Evolution
worldscientific.com
Now accepting applications for our 2027 Simons Graduate Fellowships in Ecology and Evolution! These awards support students entering U.S.-based Ph.D. programs to conduct #ecology and #evolution research. Deadline is June 30, 2026: bit.ly/4umYKZd #science
Applications for 2027 Simons Graduate Fellowships in Ecology and Evolution Now Open
The Simons Foundation’s Life Sciences division is now accepting applications for its 2027 Simons Graduate Fellowships in Ecology and Evolution.
bit.ly
We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details: asherleeks.com/apply #socialviruses #evosky #virosky 🧪
Phage community: our plasmids for executing phage transposon mutagenesis are now on AddGene and I would love for you to try it out! It is powerful for ID'ing all essential genes and knocking out all non-essentials in a single experiment :) New exp here: www.addgene.org/browse/artic...
Thrilled to share that my first dissertation chapter is now published at Ecology! dx.doi.org/10.1002/ecy.... We embed TPCs into population dynamics to show how changing temperatures' ordering — not just its distribution — increases extinction risk (i.e. heatwaves matter!) @esajournals.bsky.social
The Social Lives of Viruses is coming to Vancouver, Canada, from 4th-8th August 2026! This is a free meeting dedicated to all aspects of virus-virus interactions & evolution. To apply: socialviruses.zoology.ubc.ca @sociovirology.bsky.social #socialviruses #evosky #lovevirology #virosky
In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut? TLDR: Not much overall, in specific bacterial species. 🧵 www.biorxiv.org/content/10.6...
Species-specific prophage induction by ciprofloxacin in human gut metagenomes
Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut. Importance Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations. ### Competing Interest Statement The authors have declared no competing interest. NIH Common Fund, https://ror.org/001d55x84 Natural Sciences and Engineering Research Council
biorxiv.org
Capturing dynamic phage–pathogen coevolution by clinical surveillance "we capture the acquisition of a parasitic anti-phage mobile genetic element, PLE11, that initiated a selective sweep coinciding with the largest cholera outbreak in recent records. " www.nature.com/articles/s41...
Capturing dynamic phage–pathogen coevolution by clinical surveillance - Nature
The acquisition of a parasitic anti-phage mobile genetic element, PLE11, showing potent anti-phage activity against cocirculating ICP1, and the subsequent evolution of ICP1 to escape this defense, are...
nature.com
The Trojan Horse is real, and it’s microscopic! 🐴🦠 Our paper is out today in @cellcellpress.bsky.social! We discovered that deltaviruses physically hide INSIDE helper viruses to sneak into new cells. And to prove it, we had to image them from every angle. 🧵👇 www.sciencedirect.com/science/arti...
Deltaviruses spread through a viral Trojan Horse
Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…
sciencedirect.com
Next one in a storm of preprints from our lab's amazing scientists.. Recent-ex-postdoc, #newPI @cathyhernandez.bsky.social studied thermal ecology of marine bacteria isolated near New Haven. Turns out, response of this bacterium to temperatures is shaped by prophages! #phagesky #microsky
Cathy Hernandez@cathyhernandez.bsky.social · 6mo agoExcited to share a preprint of work from my postdoc with @paulturnerlab.bsky.social exploring how prophages can impact host thermal ecology and evolution. www.biorxiv.org/content/10.6...
Excited to share a preprint of work from my postdoc with @paulturnerlab.bsky.social exploring how prophages can impact host thermal ecology and evolution. www.biorxiv.org/content/10.6...
biorxiv.org
Congrats to @noahhoupt.bsky.social for this massive effort (1000 generation!) evolution experiment demonstrating the importance of organism-derived environmental modifications in shaping adaptive evolution. A great example of how bacterial evolution only makes sense in the light of phage :)
Noah Houpt@noahhoupt.bsky.social · 6mo agoInterested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages?? Check out our latest preprint, now up on BioRxiv! biorxiv.org/content/10.6... For a quick summary, peep the thread below...🧵 (1/10)
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
academic.oup.com
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.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
biorxiv.org
Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
The Lancet Microbe@lancetmicrobe.bsky.social · 10mo agoNew research article Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis www.thelancet.com/journals/lan... #IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
Very happy to share that I will be starting as an Assistant Professor in the department of Biological Sciences at the University of South Carolina in January! My group will be working on environmental phage ecology and evolution, and I am recruiting for the upcoming year (more info below).
I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below. #socialviruses #evosky #virosky 🧪
The social lives of viruses | Asher Leeks | TEDxNewEngland
YouTube video by TEDx Talks
youtube.com