Our new collaborative work led by @taliamycota.bsky.social Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social and collaborators: @plantricia.bsky.social et al. tinyurl.com/5yx2wmz5 (1/n)

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

NEW pub in @science.org 🥳 Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life? For over 15 years, #phylogenomic studies have been divided. We provide new evidence suggesting that... 🔗: www.science.org/doi/10.1126/...

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny. #ProtistsOnSky #SciComm #SciSky www.cell.com/cell/fulltex...

We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO 🦠🧫

The gut MYCOBIOME is akin to the tiny group of kids in the corner of a huge homecoming dance. Their story is largely unknown. In our latest, @emilyvansyoc.bsky.social dives into the evolutionary associations of gut fungi with @erdavenport.bsky.social & Andres Gomez journals.plos.org/plosbiology/...

What determines the human gut fungal community? @emilyvansyoc.bsky.social @erdavenport.bsky.social @symbionticism.bsky.social &co present the first #GWAS of human genetic loci that influence the abundance of gut #fungi, linking these to disease risk #mycobiome @plosbiology.org 🧪 plos.io/42bCKou

We published a new lane of research today on human gut fungi. Shout out to 1st author @emilyvansyoc.bsky.social sky.social & @erdavenport.bsky.social For 20 years, bacteria received the lion's share of interest in the human gut. Yet we know little about the gut mycobiome. doi.org/10.1371/jour...

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs: probgen2026.github.io Please help spread the news.

Microbiology professor, want to join a slack for microbiology professors, any career stage, diverse career types (pure teaching, med school, R1, community college, pure research fed PIs, ...) Message me for an invite link if you are interested. No imposter syndrome, if you are 1% micro, join!

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Job is up, consider joining us! psu.wd1.myworkdayjobs.com/en-US/PSU_St...

Come to work with us! We have 2 PhD positions: 1: On stability of gut microbiome in longitudinal well phenotyped adult cohorts: tinyurl.com/MicrobiomeExpo… 2: On integrative multi-omics analysis in a unique longitudinal mother-infant cohort. tinyurl.com/EarlyLifeOmics

Very proud of my graduate student Naomi Huntley for being selected to participate in this internship!

Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...

Opening for a #postdoc in the lab available immediately. Please spread the word. DETAILS HERE: jobrxiv.org/job/baylor-c... cc: #academicJobs #postdocJobs #microbiome #Celegans #organoids #IBD #PathSky #Medsky #AcademicSky 🧪 🧬 🦠

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2 academic.oup.com/bioinformati... #jcampubs

🚨 I’m hiring a postdoc for Fall 2025 with experience in microbial ‘omics data analysis and phylogenetics/genomics. Projects will be centered around ancient microbial ecology & evolution. Click here for more information: bpb-us-e1.wpmucdn.com/wp.txstate.e... Please share, thank you 🙏🏻

A poem for my last day working at the writing center for the semester (by Joseph Fasano)

It’s Thursday! Episode #91 of #MattersMicrobial is up. Dr. Emily Davenport of Penn State joins the #QualityQuorum to discuss how host genetics impacts the microbiome. Please spread the #GoodMicrobialWord! @microbe.tv @asmicrobiology @univpugetsound youtu.be/5c7lxC1mHxk?...

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Yes, it's Thursday! Time for Episode 90 of #MattersMicrobial. Dr. Francisco Dini Andreote of Penn State joins the #QualityQuorum to discuss how the plant microbiome can be used in agriculture. Please spread the #GoodMicrobialWord. microbe.tv youtu.be/krQGvMggA3Y?...

We have a starter pack! Follow along and DM if you are part of the OHMC and would like to be added: go.bsky.app/7X9RRT2

Pennsylvania could lose $973 million due to federal health research cuts. Visit scienceimpacts.org to learn more. scienceimpacts.org

PhD Timeline xkcd.com/3081

Know any soon to graduate or recently graduated postbac researchers interested in / with experience working with phages? We are hiring a junior specialist/research tech! Apply here: aprecruit.berkeley.edu/JPF04863 (start date more flexible than stated in ad!)

Come and work with me! The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists Link below 👇

This is high art

www.nytimes.com/2025/04/03/o... Really important piece to share widely. Too many Americans don’t know how severe a threat this Administration poses to our scientific infrastructure, global leadership, and health security

OUT NOW: Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice #microsky #microbiomesky 🧪 www.nature.com/articles/s41...

🚨 Paper alert: our multidisciplinary team emphasizes the importance of microbes 🦠 in conservation of biodiversity and ecosystems🌱. We also encourage studying their ecological functions! 🧪🧫 authors.elsevier.com/c/1kjAVB8cd4...

Lab mice (domesticated for >100y) have kept gut bacterial strains that codiversified w/ rodents for >25My. Here, authors show genetic drift occured in the lab, leading to loss of microb diversity+more deleterious mutations, impacting microbial fitness in lab vs wt mice www.nature.com/articles/s41...

🚨PA colleagues: "Senator Fetterman wants to hear from you about how the federal funding freeze is affecting Pennsylvania." "If your project has been impacted, please fill out our constituent impact form:" forms.office.com/g/mFv2JAPxpC Get out your Other Support and share that info!

New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social ! Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families. doi.org/10.1101/2025...

I lost my job at the National Science Foundation yesterday, along with 167 of my colleagues, including some dear friends. This was the best job I've ever had, and I thought it would be my last. The PI community has been sympathetic and supportive, without exception. I will miss working for you.

Passionate about open science and FAIR data principles for microbiome data? Consider becoming an NMDC Ambassador next year! I was an Ambassador in 2023 and happy to answer any questions about the experience!

🧪🧬🔬◼️ !!happy international day of [redacted] and [redacted] in science!! ◼️🔬🧬🧪

Many people, including academics, don't understand what F&A is for. Please share to help. 1) Translate to "overhead" in common business accounting: 60% IDC => 60/160 = 37.5% overhead (low!) 2) Infographic explaining what it's for, linked here: www.cogr.edu/sites/defaul...

Government isn't a business. The goal isn't to save money. Success isn't measured by budget surplus. The goal is to spend money, investing in society. Every dollar spent on education, healthcare, and science is an investment in our collective wellbeing.

ATTENTION If you are someone who had an F31-Diversity (or similar) application submitted this cycle, please DM me here, contact me on signal (jeremymberg.78), or email me at [email protected]. I will keep all information confidential. 2/n

I usually reserve this account for my personal views; but today I want to represent my position as President of @asn-amnat.bsky.social to post a message that will shortly go out to the membership of the American Society of Naturalists from the ASN Executive Council

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

Our newest highlight video features groundbreaking #microbiome #art collaborations happening here Penn State University! 🧫👩‍🎨📽️ #SciArt The video features interviews with @pennstateadri.bsky.social researchers Cynthia White, Cristin Millett, and Andrew Hieronymi. www.youtube.com/watch?v=4jw-...

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...

We are so grateful to everyone who has reached out to offer support as we face this horrifying tragedy. We have a long road ahead and are comforted to know we are not alone. If you would like to contribute: gofund.me/95387a92

Today I had the opportunity to give a talk on my undergrad research to the One Health Microbiome Center. This was an amazing opportunity to introduce this collab to the center. Huge thanks to the One Health Microbiome Center at PSU, Emily Davenport @erdavenport.bsky.social, and Claire Thomas!

Proud of undergrad @marialovallo.bsky.social who gave a research lightning talk at the @psumbiome.bsky.social Networking Event this afternoon. She's single-handedly driven this collaboration between my and Thomas labs identifying how the microbiome shapes flight phenotypes in Drosophila 🪰

Today I learned…