Margaret Alexander

Congrats Joel! Hope all is well with you!

The role of gut microbial metabolites in the T cell lifecycle - Nature Immunology Tran et al. discuss the role of the gut microbiome and gut microbiome-derived metabolites in T cell biology.

Interesting recent review on the links between gut microbes and T-cells, highlighting a mechanistic framework linking microbial metabolites to all stages of T-cell fate and function.
🔗 www.nature.com/articles/s41...

🚨 AAI is proud to announce the launch of the AAI RESTORE Grants Program, an $8M emergency funding initiative to support scientists whose immunology-focused federal research grants were abruptly terminated or frozen in 2025.

🔗 ow.ly/rwMU50Wy3Mp

#AAIRESTORE

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!

BREAKING: A federal judge reversed National Institutes of Health's terminations of hundreds of critical research grants that were canceled because of their alleged connection to disfavored topics, including diversity, equity, inclusion, and gender identity.

This is a major win for public health.

State street, Madison WI June 14 2025

Estimated 15K+ in Madison WI
A lovely shirt seen:
One Thing Money Can't Buy: Wisconsin

Medical Research Funding — Unbreaking How the administration is breaking the government, and what that means for all of us.

New plan:
As I am getting more and more spam texts I will just respond with links about science funding like this one: unbreaking.org/issues/medic...

Week 19 What now & what’s next in science and higher ed

Each Friday night, I write up what happened in science & higher ed.

- 1200+ pages of new (weird) detailed budget request
- cancellation of pandemic flu & HIV vaccine efforts
- more travel visas throttled
- FEMA, “gold standard science” & more

This was week 19: buttondown.com/liminalcreat...

Help Protect the Future of UW–Madison Research Badger-led research strengthens communities, saves lives, and supports thousands of jobs. Learn why this work matters—and how you can support it.

From helping farmers plan with better weather data to growing Wisconsin's semiconductor industry, discover some of the ways that @uwmadison.bsky.social research is improving lives and making the U.S. stronger. #WisconsinInnovates

A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance Clostridioides difficile, a major cause of antibiotic-associated diarrhea, is suppressed by the gut microbiome, but the precise mechanisms are not ful…

New research from @jordanbisanz.bsky.social et al. used machine learning to design C. difficile suppressive synthetic microbiomes. 🦠

This is a big step towards reducing antibiotic use & making a safer and more effective fecal microbiome transplant alternative.
www.sciencedirect.com/science/arti...

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:

Week 3 Figuring out what to focus on now & what to focus on next in science and higher ed

Well. I have been informed that it is the weekend, again.

When you are ready to sit down together & figure out what just happened and what to do, we’ve got you: buttondown.com/liminalcreat...

It’s also okay if you’re coming in hot! “What the actual fuck??” is a sensible start place at the moment.

Starting my Bluesky adventure by highlighting a new paper from the lab!

Revised and Extended: What's Happening Inside the NIH and NSF

I’ve unfortunately needed to add more material to my post from yesterday. The re-election of Donald Trump is looking like the biggest act of American self-destruction since the Civil War.

Same link, new title and some updates.

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Happy to share our new paper in @naturemicrobiol.bsky.social on mapping spatial relationships of the human gut microbiome. We identified distinct spatial hubs between gut bacteria that reflect sub-community assemblies at the micron-scale. Led by Miles Richardson & co.
www.nature.com/articles/s41...

ASM website screenshots from the wayback machine in December '24 (web.archive.org/web/20241211...) vs today. Pretty disappointing!! 🧪

Expanding the human gut microbiome atlas of Africa - Nature A cross-sectional study from four African countries shows the importance of investigating the gut microbiome in previously under-represented populations and provides a framework for equitable microbio...

Out now in @nature.com: Gut microbiome diversity across African populations - a valuable resource for further research and foundational for global health equity. 🧪

www.nature.com/articles/s41...

@lizneeley.bsky.social is publishing a weekly newsletter to track the ongoing attacks in science and higher ed. If you want to keep abreast without drowning in the news, I recommend it: buttondown.com/liminalcreat...

Integration of 168,000 samples reveals global patterns of the human gut microbiome The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

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...

Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation Is it possible to restore the human gut microbiome in industrialized settings and reintroduce microbial species that have been lost? In healthy adults, Li et al. found that consuming a diet mimicking ...

Our study @cellpress.bsky.social finds healthy Canadians that consume a non-industrialized-type #diet can modulate their #microbiome, boost beneficial metabolites and improve their health. In just 3 weeks:

LDL cholesterol ↓17%
fasting glucose ↓6%
CRP ↓ 14%

www.cell.com/cell/fulltex...

We are hiring a new faculty member in my dept at Minn State Mankato! This person will teach human anat/phys for bio majors and run a research program with undergrad and M.S. students. I'm happy to answer questions about what it's like here as new faculty!

✋We're working on some diet-microbiota-immune interactions in multiple sclerosis! Would love to be added - thanks for organizing!

Always notable when the Lamming Lab drops more insight into the geroprotective effects of BCAA restriction. Never thought I’d say isoleucine is the coolest of the 3, but it is clearly super important! 😎 Awesome work!

Thanks Erik! Hope you're doing well!

Huge shout out to Kevin Whelan and Maria Marco who spearheaded this work and to all the co-authors for their contributions! It was a pleasure getting to work with you all!

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome - Nature Microbiology Here the authors make recommendations for the design of clinical trials for prebiotics and probiotics that includes consideration of diet and the gut microbiome.

Diet profoundly impacts the composition and function of the microbiome having consequences for health and disease. Therefore, it is important to consider diet and the gut microbiome when designing and reporting prebiotic and probiotic clinical trials. See our recent perspectives on recommendations:

Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme Bae et al. uncover that a highly transcribed member (Gp Hcdh) of the gut bacterial catechol dehydroxylase family metabolizes hydrocaffeic acid, an abundant anti-inflammatory polyphenol. Analyses of hu...

Congrats to Min Bae and the Balskus Lab on their new study! Min used a Metatranscriptomics-guided approach to find a microbiome enzyme involved in the metabolism of hydrocaffeic acid. Glad I could be involved in this fascinating study! Check it out here: www.cell.com/cell-host-mi...

Hi everyone, I tried assembling a Microbiome & friends starter pack.
🦠🧫🔬

Still learning to use bluesky and might have missed you, let me know if you would like to be included.

go.bsky.app/Fq36egy

Another starter pack of fine fine folks - New PIs! We're all figuring it out together! Please do (self-)nominate

go.bsky.app/KJXNgfZ