2022 Tweet from Caroline Keroack: "I have a whole PhD I whisper to myself, as I write C1V1 = C2V2 on a paper towel for the 8000th time."

This tweet is all of us.

That's good.

Why why are we still using MDA on viral enrichments? It biases your data so sharply to ssDNA genomes. It's gotten to the point i can look at an abundance graph and guess quite accurately if they used the Genomiphi kit. I get DNA yield is low, but this can't be the best way.

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

We hope this publication can be used as a tool by wet lab and dry lab scientists alike to enhance research and push the field of viromics forward! 🦠

We also outline a typical computational workflow to predict and characterize viral genomes from metagenomes, including our recommendations for best practices!

Validation can look like:
🦠 isolating a phage of interest through classic methods/viral tagging
🦠 use of classic or modern phage techniques to interrogate phage-host interactions
🦠 visualizing interactions or virion structure with microscopy
🦠 using germ free models to interrogate mecha

Amazing discoveries have been revealed by characterizing how gut viruses modulate, and how they are modulated by, host health. But! We argue this can be taken a step further by using and developing wet lab techniques to validate sequencing results.

Tools and approaches to study the human gut virome: from the bench to bioinformatics | mSystems The human gut microbiome is a complex community of bacteria, archaea, fungi, protozoa, and viruses that reside within the gastrointestinal (GI) tract (1). Notably, much of the literature regarding the...

Super excited to share my latest publication with Justin Malogan and @suez.bsky.social , my love letter to viromics! 🦠 Here, we discuss computational and wet lab methods to study the gut virome and how they can be used together

But why is this synergy so important?
journals.asm.org/doi/10.1128/...

Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com

Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.

Exclusive: US FDA launches fresh safety scrutiny of approved RSV therapies for infants U.S. health regulators informed senior executives at Merck, Sanofi and AstraZeneca last week that their approved protective RSV treatments for infants would face fresh safety scrutiny following concer...

Acting CDER Director Tracy Beth Høeg is not wasting any time ensuring that babies are as vulnerable as possible to preventable diseases that kill them.

Now she's going after preventive RSV meds based on unverified claims from an anti-vax blogger.
www.reuters.com/business/hea...

Excited to share new work from @cultivarium.bsky.social on genetic tools (plasmids, inducible promoters, transposases, + more) for Sporosarcina pasteurii.

S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:

Come for the compelling science, stay for the gorgeous pictures of assembly graphs.

(COI: I'm a co-author ;)

An enteric virus can replace the beneficial function of commensal bacteria Intestinal microbial communities have profound effects on host physiology1. Whereas the symbiotic contribution of commensal bacteria is well established, the role of eukaryotic viruses that are present in the gastrointestinal tract under homeostatic ...

I’ll start! Here they asked, can viruses replace the function of gut bacteria in germ free mice? pmc.ncbi.nlm.nih.gov/articles/PMC...

What is your favorite gut microbiome paper that started with a simple question but ended with super cool results? Drop them below 🥰

Ty Claire 🥰

The tension between me and this chocolate chip sourdough i stress baked is 👀🥵

and there it is

Barbara McClintock portrait

🧬🌽 Happy Transposon Day! 🌽🧬

Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study.

Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social

bsky.app/profile/bapt...

Needless to say my lab will never allow me to miss a group photo 💚 😂 @suez.bsky.social

Right before this he was above us singing

Pls enjoy this little Prothonotary warbler that was showing off this morning 🐤

Telomere bacteriophages are widespread and equip their bacterial hosts with potent interbacterial weapons Klebsiella host strains infected with telomere phages can grow to be the dominant lineage in mixed populations.

"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors”

www.science.org/doi/10.1126/...

Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis - Nature Medicine A novel personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off may represent a viable alternative approach for the treatment of antimicrobial-resistant bacteria...

A phage therapy using naturally occurring bacteryophages that not only kill but also selects for less resistant bacteria, shows promise in Cystic Fibrosis patients infected with drug resistant Pseudomonas. Kudos Dr. Chen, Stanley, Turner and Koff!!!
#ScienceMatters
www.nature.com/articles/s41...

Biomedical Research: Keeping America’s Edge in Innovation | United States Senate Committee on Appropriations United States Senate Committee on Appropriations

www.appropriations.senate.gov/hearings/bio...

AI-generated (ChatGPT) cartoon of different gut bacteria munching on different types of sachets containing "fake sugar" as a reference to non-nutritive sweeteners

Do non-nutritive sweeteners alter the human microbiome? And why is this question important?

Check out our new review in Immunometabolism, spearheaded by @kcrakes.bsky.social, Lauren Questell & @subah.bsky.social and quick 🧵👇:

journals.lww.com/immunometabo...

NSURP.org National Summer Undergraduate Research Project

Just signed up to be a mentor for the National Summer Undergraduate Research Project #NSURP2025 #nolabnoproblem www.nsurp.org - if matched, this will be the third year we host a @nsurp.bsky.social scholar in the lab and @haleybiont.bsky.social and I are excited to meet them!

Maybe because I'm still early in my career, but I feel *so honored* when someone i mentor asks me to write a letter for them!

Suez lab and their 3D printed phages! (left to right) Jotham, Haley, Justin, Yingying, Chinmay, Katti, Jason

Had so much presenting at @camri-igs.bsky.social this year! Featuring some phree phage swag!! 🦠