and there it is

🧬🌽 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

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

"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/...

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...

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...

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!

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

Super proud of our postdocs @kcrakes.bsky.social & @haleybiont.bsky.social for their outstanding talks at @camri-igs.bsky.social Mid-Atlantic #Microbiome Meeting, featuring exciting science from all over the region + keynotes by Sue Lynch (UCSF) & @benwolfe.bsky.social (Tufts) + phage swag! 😎 🦠

I try to maintain a professional presence on this app and keep personal updates to a minimum, but I'm proud to announce @haleybiont.bsky.social and I became Discus grandparents over the weekend!

Im so proud of you Annie for using your voice! It matters! 🩵

Big article about the protests tomorrow, which mentions that they were organized on Bluesky!

The way I watched the same men who said a woman was too emotional to be president throw absolute *temper tantrums* in the Oval Office yesterday 🪦 so anyway happy Women’s history month 👩🏻‍🔬

So excited to share this latest work by @kelseyhuus.bsky.social !!! She shows that flagellin in the human gut affects whether or not people develop fever in response to vaccine, and the amount of flagellin reflects diet

any other postdocs feeling existential about science today 🥲 it is so hard to do stuff

Johns Hopkins officials said the NIH funding cut puts at risk approximately 600 current and ongoing clinical trials at Hopkins, including open clinical trials in cancer, pediatrics and children’s health, heart and vascular studies and the aging brain. www.thebaltimorebanner.com/education/hi...

It should not need to be said that using AI to review grants is utterly stupid and will lead to choosing the most boring and average grants — humans still do way better than AI on expert tasks.

Great reporting in this article! And some of my NSF postdoc cohort bravely speaking out on the record! We cannot let these illegal and unjust attacks on science continue. www.washingtonpost.com/science/2025...

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

Stress baking the existential dread away (sourdough glazed donuts) 🍩

I want to expand on the extent to which IDEAA materials have been purged: I wrote an article last year for women’s history month on the history of women in antimicrobial development….DELETED.

ASM did a spotlight article on me last February and it has also been taken down as “under review”. Other spotlight articles are still up so not sure how else to interpret this besides the obvious. It feels pretty crappy to have been singled out and I won’t be engaging with them in the future.

I’m on one of ASMs IDEAA committees and we have received 0 communication from ASM staff on why this is happening. I had to find out via social media. Extremely disappointing.

ASM … amidst the darkness here goes yet another safe place for American scientists 😓

🧵 STATEMENT: WHO expresses deep concern on the implications of the immediate funding pause for #HIV programmes in low- and middle-income countries. These programmes provide access to life-saving HIV therapy to more than 30 million people worldwide. Read more bit.ly/42yxxIz 1/5

If you’re at a European institution and are looking to poach American scientists, this would be a very good week to do it

sometimes its worth looking at documentation because you find little easter eggs like this 🥰

“‘It’s very easy to assume that science is going to change organically towards equality — and what this study shows is that that’s not happening…It is an ‘important reminder for us that we need to stay vigilant in working towards equality in science’” @crsugimoto.bsky.social 🧪 #AcademicSky 👩🏽‍🔬

I am begging, PLEADING! with journals to put figures in line with the text for peer reviewers 💋 it’s madness

OUT NOW Unraveling viral ecology and evolution over twenty years in a freshwater lake @karthik-a.bsky.social & co www.nature.com/articles/s41...

Beautiful work by Thomas Pitot as well as by @simrouxvirus.bsky.social, @ai-cy.bsky.social, @vincentsomerville.bsky.social, et al. ! academic.oup.com/ismecommun/a...

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3 www.science.org/doi/10.1126/...

If you’re looking for a protist-forward holiday gift for someone who also likes New Jersey (very niche, I know), these are now for sale in my little online store! www.couchmicroscopy.com/store

I wrote about the backstory of our recently published metagenomic profiler called sylph (www.nature.com/articles/s41...), partially to celebrate the new migration to bluesky Check out the blog here: jim-shaw-bluenote.github.io/blog/2024/de... -- and I apologize in advance for the lack of brevity :)

tagging #MicroSky #PhageSky

Obesity imprints adipose tissue even after weight loss - promoting regain and progression. Same is observed with GLP-1 therapies were we see regain in the majority of individuals who stop TX www.nature.com/articles/s41...

Targeted protein evolution in the gut microbiome by diversity-generating retroelements www.biorxiv.org/content/10.1... Nice paper on diversity generating retroelements in the Bacteroides:

Looking for advice! I'm interested in trying to identify (more robustly) eukaryotic viruses in gut metagenomes. After my typical virome workflow (virsorter -> checkv -> etc..) what annotators/databases would you use? are we even at a place where we can trust annotations for euk viruses? TIA 💕

‼️Sequencing friends! Does anyone have experience or insight on sequencing gut metagenomes (or any metagenome) on the Novaseq 6000 vs Novaseq X Plus platforms? Are the quality and quantity of reads really equivalent? I appreciate any help ☺️

Introducing vClassifier, a new tool for species-level classification of phage. We analyzed conserved genes in viral lineages and leveraged them for fine-scale taxonomy. www.biorxiv.org/content/10.1...

Here is some recent work we've been doing at Cultivarium on detecting methylation patterns with nanpore. We find that nanopore's modified basecalling models works well - if you have recently sequenced a prokaryotic isolate you can use MicrobeMod to ID methylation: www.biorxiv.org/content/10.1...

Just got this from a labmate of mine who does no sort of computational work lol

Rapid bacteria-phage coevolution drives the emergence of multiscale networks www.science.org/doi/abs/10.1... #jcampubs