Connor Tiffany

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥

I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com

@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social

www.cell.com/cell-systems...

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This is fantastic work and I'm excited to see it in press! Congrats to all involved!

Happy to see that this fantastic work is in press now! Congrats to the Palmer lab and lead authors @xiaomeiren.bsky.social and @rmasonclark.bsky.social.

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
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I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.

Excited to share this collaborative study with @ritatamayo.bsky.social showing that E. faecalis influences C. diff morphology through the phase variable CmrRST system! This work was co-led by the amazing team of @ashleyweiss.bsky.social and Jilarie Santos-Santiago!

This is anectodal, but for my own coding the only things that AI can do correctly I can do quicker than it takes to write a prompt that generates something useful. I figured productivity gains were over hyped but yikes lol

Philly will stop functioning if these cuts happen, and if Philly doesn't function, Pennsylvania's economy will crash and burn.

The Republican majority leader's comments about 300 million being too expensive of an investment while the state has a deficit makes about as much sense as a marathon runner in second place deciding to amputate their legs because they increase the need for blood flow and oxygen.

WTF is this - why is NPR quoting some obscure health policy guy from a think tank both sides-ing miasma theory?

Hey @npr.org, "strengthening" ones immune system with healthier habits won't prevent a measels infection. If you lack the expertise to challenge the validity of a statement ask an actual scientist. Embarrassing to end this piece like that. Also, the miasma theory isn't just outdated, it's false.

This should absolutely be a scandal which people lose their jobs over. You'd have to assume that anyone in power actually cares though to think that would happen, which obviously would be a bold assumption in present circumstances.

There is no "science-wide replication crisis" because every word in that phrase carries unfounded assumptions. 🧵

1. There is no evidence that progress has generally stalled in the sciences. Also, no one has actually tried to estimate replicability across fields.

Excited to share our new work in @aga-gastro.bsky.social! We show that dietary fiber alters the window of susceptibility to C. difficile following antibiotic exposure. This really fantastic study was co-led by an amazing team @rinniehewlett.bsky.social @alhecht.bsky.social and Amanda PeBenito.

Delighted to announce the @keystonesymposia.bsky.social meeting: Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection. Join us in Breckenridge in May 2026!!

You can check out the program and amazing lineup of speakers below: keysym.us/KSAntibiotics26

#KSAntibiotics26

Hopefully more universities do the same. Nice to see some good news for once.

Thrilled to share our @elife.bsky.social paper "Inflammasomes primarily restrict cytosolic Salmonella replication within human macrophages" by 1st author Dr. @marisaegan.bsky.social (@cambupenn.bsky.social alum, now faculty @swarthmorecollege.bsky.social)! elifesciences.org/articles/90107 🧵(1/n)

Short-term alterations in dietary amino acids override host genetic susceptibility and reveal mechanisms of Salmonella Typhimurium small intestine colonization In addition to individual genetics, environmental factors (e.g., dietary changes) may influence host susceptibility to gastrointestinal infection through unknown mechanisms. Herein, we developed a mod...

Can genetic resistance to Salmonella be impacted by dietary changes? We use a genetically resistant 🐭 to explore diet-microbiome-pathogen interactions and mechanisms of Salmonella Typhimurium small intestine colonization. Awesome work by grad student Nic Shealy!

www.biorxiv.org/content/10.1...

The psychology of it has me at a total loss as well. Do the people who support things like this have nothing that brings them joy in this world other than hurting their perceived enemies? Hobbies, interests, etc.

One of my favorite films and very spot on about the danger of tech bros having access to/control over anything important 🙃.

For me it's actually the opposite, I find functionals more readable than for loops, but agree that for loop's bad reputation in R is undeserved. Sometimes it's the best tool for the job.

Are universities going to start speaking up? Because if they think Trump pulling back federal dollars is an existential threat, they should see what happens when no international students want to come here for fear of ending up in a MAGA concentration camp.

Rewilding catalyzes maturation of the humoral immune system Releasing laboratory mice into the natural environment enhanced maturation and activation of the humoral immune system.

Congratulations Ying-Han Chen and Kim Zaldana for showing how B cells are altered when lab mice 🐭 are released outdoors! www.science.org/doi/10.1126/...
Here’s some context for the paper followed by how gov’t 💰 + other sources combine to make these types of studies possible 1/n

We are experiencing an assault on science unparalleled by anything I’ve seen in my life. It’s not one issue or another anymore, the entire institution is under attack by the most powerful individuals in the country.

This Friday, where will you be?

standupforscience2025.org

Transmission of Staphylococcus aureus in the neonatal intensive care unit predicts invasive infection Background Staphylococcus aureus is a leading cause of healthcare-associated infection and is one of the most common pathogens causing serious invasive infection in the neonatal intensive care unit (N...

Excited to share our work with @pjplanet.bsky.social and @ahmedmicrobes.bsky.social tracking Staph aureus transmission across the NICU using genomics!!

This study was co-led by the amazing @qianxuan.bsky.social and Lakshmi Srinivasan, and made possible by the @centermicrobialmed.bsky.social

Inside the Collapse at NIH Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.

By @katherinejwu.com

"The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,”

The NIH is in a struggle for its (and our) lives. This is existential to America:

Are academic institutions unaware that this is happening? We are in the middle of study section season. This seems like an incredibly urgent problem that requires more lawsuits.

Metagenomic estimation of dietary intake from human stool - Nature Metabolism Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...

#metagenomics #microbiome #microbiomesky

So what is MEDI? A combination of two things:

This is incredibly cool work. Congrats to all authors involved!