Cathy Hernandez

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.

15.10.2025 21:40 — 👍 183    🔁 75    💬 7    📌 3

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...

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/...

12.10.2025 21:16 — 👍 86    🔁 50    💬 1    📌 2

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 📈

10.10.2025 13:12 — 👍 63    🔁 26    💬 2    📌 1

Thanks Mike 😊😊

09.10.2025 13:49 — 👍 1    🔁 0    💬 0    📌 0

Thanks Noah 😭😭

09.10.2025 13:49 — 👍 1    🔁 0    💬 0    📌 0

A group of people celebrating with drinks outside of a bar in New Haven, Connecticut.

A group of people with the Yale mascot Handsome Dan in front of a coffee truck.

A photo of a professor and two trainees standing behind a table of two pies at a going away celebration.

So many people to thank, but I am particularly grateful to my mentors @bkoskella.bsky.social and @paulturnerlab.bsky.social for their support over many years. I am so so sad to be leaving the wonderfully supportive Turner lab, but excited to start a new chapter.

08.10.2025 16:34 — 👍 8    🔁 0    💬 0    📌 0

Study - Department of Biological Sciences | University of South Carolina

I am recruiting graduate students (MS and/or PhD) for the upcoming fall semester (more info here: tinyurl.com/35p6hfx7), and will soon be hiring a research associate/technician (details TBD).

08.10.2025 16:34 — 👍 6    🔁 4    💬 1    📌 1

We will be studying the effects of environmental factors on non-model marine phage-host interactions, with a particular interest in the causes and consequences of context-dependent prophage dynamics. If you are interested in tackling these questions, please reach out!

08.10.2025 16:34 — 👍 4    🔁 0    💬 1    📌 0

A graphic advertising phage ecology and evolution research at the University of South Carolina, showing a central image of a tide pool flanked by a photo of an agar plate containing diverse microbes and a TEM image of a virus particle.

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).

08.10.2025 16:34 — 👍 75    🔁 27    💬 6    📌 2

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 🧪

07.10.2025 22:38 — 👍 39    🔁 15    💬 0    📌 1

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

27.08.2025 12:24 — 👍 74    🔁 37    💬 2    📌 2

Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...

Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...

25.08.2025 14:33 — 👍 60    🔁 24    💬 3    📌 1

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

12.08.2025 15:53 — 👍 159    🔁 60    💬 4    📌 5

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

22.07.2025 15:06 — 👍 84    🔁 41    💬 2    📌 2

For #ASMicrobe folks - looking forward to a busy phage day on Sunday!

20.06.2025 19:06 — 👍 14    🔁 7    💬 1    📌 0

Filamentous cheater phages drive bacterial and phage populations to lower fitness Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...

Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...

02.04.2025 12:41 — 👍 59    🔁 39    💬 7    📌 2

Schematic of probability distribution of the latent period along with single-cell examples of bursts that increase in magnitude as the latent period increases. Full details in the paper.

New on #biorXiv: 'Inferring single-cell heterogeneity of bacteriophage life-history traits from population-scale dynamics'. A theory-experiment collaboration, led by @mariandm.bsky.social + Ran Tahan w/the Lindell group at Technion (and yes, I am excited).

a 🧵

www.biorxiv.org/contenat/10....

26.03.2025 14:29 — 👍 24    🔁 13    💬 2    📌 2

Combinatorial phenotypic landscape enables bacterial resistance to phage infection Success of phage therapies is limited by bacterial defenses against phages. While a large variety of anti-phage defense mechanisms has been characterized, how expression of these systems is distribute...

How can single-cell transcriptomics profile phage infection in individual microbial cells? Check out our preprint with Anika Gupta, Norma Morella, Dmitry Sutormin & other authors, in collaboration with Georg Seelig (UW) and Neel Dey (Fred Hutch). www.biorxiv.org/content/10.1...

16.01.2025 02:26 — 👍 28    🔁 20    💬 0    📌 3

Bright green spots are phages (viruses), bacteria are the faint rods in light blue.

We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠

The paper was posted online today:
www.pnas.org/doi/10.1073/...

#phagesky #microsky

19.12.2024 22:10 — 👍 76    🔁 30    💬 3    📌 2

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...

12.12.2024 19:22 — 👍 182    🔁 98    💬 5    📌 11

Phage friends - hope to see you all next year in LA!

23.11.2024 17:25 — 👍 2    🔁 0    💬 0    📌 0