Emily Davenport

So excited to have this study live! Lead by @ee-reh-neh.bsky.social's teram and in collaboration with an incredible team at MRIN in Indonesia. This is the culmination of ~5 years of work including a ton of effort in the field. Really proud of how this came together!

www.biorxiv.org/content/10.6...

Medicine’s J. Arvid Ågren examines how organisms persist with internal conflicts | CWRU Newsroom | Case Western Reserve University J. Arvid Ågren, PhD, assistant professor at Cleveland Clinic Lerner College of Medicine, and Manus M. Patten, teaching professor at Georgetown Univer...

The Paradox of the Organism in the university news

case.edu/news/medicin...

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)

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

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/...

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

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...

Selection and transmission of the gut microbiome alone can shift mammalian behavior Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...

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
🦠🧫

Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates Fungi in the gut microbiome (the "mycobiome") are a neglected component of the human holobiont. This study of gut fungal profiles across natural populations of humans and non-human primates reveals si...

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/...

Human fungi-associated variants (FAVs) associate with 9 fungal taxa and overlap protein-coding genes. A Manhattan plot shows all FAVs and their associated fungal taxa at the three significance levels (exploratory, black; genome-wide, red; study-wide, blue).

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

Gut fungi are associated with human genetic variation and disease risk In contrast to decades of research on gut bacteria, human genetic determinants of the gut fungal community (mycobiome) remain understudied. This investigation presents the first GWAS on the number and...

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!

Student-led experimental evolution reveals novel biofilm regulatory networks underlying adaptations to multiple niches We established a research-education partnership known as EvolvingSTEM that provides secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution....

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...

Postdoctoral Associate in IBD genetics in C. elegans and organoids Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

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 AbstractSummary. PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference gen

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?...

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

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

Such bullshit. I’m so sorry you’re dealing with this

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

SCIMaP - Impacts of Federal Cuts to Science and Medical Research Developed by an interdisciplinary research team, this website shows how funding cuts reduce economic activity and employment nationwide

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

PhD Timeline xkcd.com/3081