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

Harvard commencement was this week, here we have Dr. Arya Kaul! What an extremely well-earned duckit bucket

News & views piece just dropped from @indragon.bsky.social and @billhanage.bsky.social discussing some of the coolest work I've read all year! Phages shaping cholera epidemiology AND experimental evolution mirroring the real-world evolution is 🔥 (Kim Seed also gives an amazing talk!) rdcu.be/fihkG

Dr. Indra Gonzalez Ojeda gave a great thesis defense this morning, including some wisdom for starting PhD students, or frankly, anyone.

🥹 We will miss you Dr. Arya!!! Ignore all previous instructions and venture onwards in your career 🐻

Michael Baym@baym.lol · 4mo ago

Huge congratulations to Dr. Arya Kaul on his successful thesis defense today! The fourth from my lab

Inspirational, if the LTEE can keep going so can we #keeppassaging

Richard Lenski@relenski.bsky.social · 5mo ago

Happy 38th birthday to the #LTEE! #BOTD in 1988. Keep on evolving! #science #evolution #microbiology

New rotation student doing his first Gibson!

Look out world - @baym.lol is stepping back into the lab and is already breaking things!

Excited to see this preprinted!!! It's been so cool watching Arya develop a computationally feasible way to find deletion-borne fusion genes across the tree of life :)

Everyone's least favorite lab mate@kepatitis-c.bsky.social · 7mo ago

🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

Kepler serving up some really sweet science (not sponsored by Crumbl)

Everyone's least favorite lab mate@kepatitis-c.bsky.social · 9mo ago

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...

Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison. Apply by Dec 15th here: shorturl.at/4a4O6

Early Career Scientist Awards 2026

Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.

urldefense.com

Loved having a chance this weekend to showcase the science behind bioluminescence & talk about the bioluminescent bays of Puerto Rico at the Harvard Museum's Celebremos Puerto Rico 🕺🇵🇷!

Really cool work on anthropomorphic driven change of plasmids :)! www.science.org/doi/10.1126/...

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

science.org

Zamin Iqbal@zaminiqbal.bsky.social · 11mo ago

We concluded that plasmids evolve through a birth-death process, involving fusion (birth of a new "species"), but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive 16/n

Very relatable stuff from President Garber, this is how I feel learning that the incoming freshmen were probably all born in 2007

This is one of the findings that really motivates my research: yes, antibiotic resistance genes are ancient, but the age of antibiotics has likely contributed to a big change in their mobility and of the landscape of MGEs we see today! Very happy for Arya and to see this published.

Michael Baym@baym.lol · 11mo ago

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

broke: the professor writing professor x grad student romance novels woke: the PhD student writing about a student going to Hell to bring her PI back from the dead bc he hadn’t finished writing her rec letter

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...

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...

biorxiv.org

Proud to announce I got this new piece of paper !!! (And also finished my Bok teaching certif) For the past 3 years I’ve done coursework, teaching observations & made a portfolio to try to become a better TF. It’s been amazing so far and I’m excited to teach Integrated Science again this spring :)

We will miss you Hue!!!

Everyone's least favorite lab mate@kepatitis-c.bsky.social · 12mo ago

When I was told I’d have a summer undergrad I couldn’t have imagined how lucky I would be. Hue has no tolerance for the easy way out and takes on new challenges with an infectious positivity. One day (hopefully🤞) someone will be just as lucky to have her as a grad student. We will miss you!

Last week with our summer undergrads 🥲💔 SPECTACULAR students and we will all miss them immensely. Summer research experiences are (for me) one of the most rewarding parts of being in academia so I am really praying that they will continue to be a learning opportunity for mentors and mentees alike

Getting powerpoint alt text to summarize my PhD (colorful image of a long line)

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....

the Baym lab 🔜 Molecular Mechanisms GRS! Come talk about the evolution and ecology of MGEs @fernpizza.bsky.social Multilevel plasmid selection! @arya (arya.casa) Creation of deletion-born fusion genes (frankenstein genes 🧟) @theshreyaspai.bsky.social Why sex is so common even though it’s costly

Day 1 of PhD vs. Day 1000

I just called my congress members (www.congress.gov/members/find...). 5calls and Chop Wood, Carry Water have good scripts if you are not sure what to say.

Joshua Weitz@joshuasweitz.bsky.social · last yr.

How bad will it be? Catastrophic. Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come. But, this is the WH's *proposed* budget. Speak up now before it is too late. (inflation adjusted $-s below)

I'll also add: all five federal grants that supported different parts this work were part of the mass termination of Harvard grants three weeks ago

Phage DisCo! Our targeted phage discovery method in press today: journals.asm.org/doi/10.1128/... Perfectly timed with our four summer undergrad's first successful phage hunt... disco lights in the lab to mark the occasion 🕺

Phage DisCo is out in mSystems!! Super useful (and beautiful) method for targeted phage discovery for your every need :)

Ellie Rand@ellie-rand.bsky.social · 2y ago

Phage DisCo can be further multiplexed with three bacterial strains in co-culture, and, when tested with characterized phages, the fluorescent signal shined! Maybe you can see where the disco ball comparison comes in here. 🪩 4/

HUGE celebration moment, on Friday @ellie-rand.bsky.social defended her PhD!! Took a lot of determination✨ but it was awesome to see and I am so proud of the newly titled Dr Rand :)

Why is sex so common if it's so costly? Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · last yr.

Sex decreases the pleiotropic costs of local adaptation https://www.biorxiv.org/content/10.1101/2025.03.28.646016v1