Dan Sprockett

This is great, thank you! The National Science Board said there would be more information about this year's GRFP today, but I haven't seen anything yet: www.youtube.com/live/qacDcWu...

As an aside: You an I are probably in a very small cohort of people who went from Kent State to Stanford+Harvard.

Students, faculty mystified as NSF turns back applications for prestigious fellowship program Applicants to a prestigious National Science Foundation fellowship program say many submissions have been mysteriously “returned without review.”

The lack of information about this has been incredibly frustrating:

Students, faculty mystified as NSF turns back applications for prestigious fellowship program
www.statnews.com/2026/02/11/n...

Another excellent piece by @jonathanwosen.bsky.social at @statnews.com

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing

Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

Sometimes you find that you need a tool that does a specific thing, and the universe just manifests it...

(...or maybe it was years of hard work by very clever colleagues).

Special Research Seminar – 12/10/2025 Daniel Sprockett from Wake Forest University School of Medicine will be visiting Duke to present some of his research to…

I'll be @dukemedschool.bsky.social next week presenting my research: “Ancient Partnerships, Modern Insights: Tracing the Assembly, Transmission, and Evolution of Mammalian Gut Microbes”.

sites.duke.edu/microbiome/2...

Come say Hi! @duke-university.bsky.social #microbiome

Poster deadline for the Keystone Microbiome Meeting in Banff is December 30th www.keystonesymposia.org/conferences/...

Will be a great meeting focused on human microbiomes, spanning basic, mechanistic, and applied. Organized by myself, @amibhatt.bsky.social , and Harry Sokol. Join us!

Proud to have contributed to this important work!

STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

"The Assembly, Evolution, and Clinical Implications of the Gut Microbiota in Early Life" With Daniel Sprockett, PhD, MSc | Center for Gastrointestinal Biology and Disease

If anyone happens to be around UNC Chapel Hill this week, I'll be speaking on Tuesday: www.med.unc.edu/cgibd/event/... @microbiomeunc.bsky.social #microbiome

Prehistoric Global Migration of Vanishing Gut Microbes With Humans The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...

Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.

Prehistoric Global Migration of Vanishing Gut Microbes With Humans The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...

Check out this incredible analysis!

Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

Looks like it'll be a good one!

Excited to share the Compendium Manager -- our new tool for scaling bioinformatics pipelines! Launch thousands of analyses, track progress, and maintain reproducibility. Developed by @richabdill.com. Check it out: arxiv.org/abs/2505.11385

Mobile integrons encode phage defense systems Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

#NatureMicroPicks

Microbial integrons in focus 🦠🧬

Two studies showing microbial integrons encoding phage defense systems

#MicroSky

www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...

One thing I think I want to ban entirely is using AI-generated citations. You can't really cite something if you haven't read it yourself.

And even if AI hallucinations get better, I think the risk is far too great.

One thing that comes to mind that could be very positive is assistance with coding and data analysis. But how do I ensure that lab members have a deep understand of how every line/function works?

A very open-ended question:

Has anyone developed a lab policy for for AI use in their biomedical research that they'd be willing to share?

Have people even thought about defining what should be allowed/encouraged, and what should be outright banned?

Please share with anyone who might have ideas.

Ecologically expanding the One Health framework to unify the microbiome sciences | mBio Microbiome research rapidly expanded in the last two decades, with nearly 200,000 peer-reviewed articles that use the word “microbiome” and significant microbial lineage discoveries reshaping the evol...

🔬 New Perspective in mBio (@asm.org)!

We call for a shift from disease surveillance to microbial stewardship, and highlight testable, cross-system hypotheses to unravel central rules of microbial life–spanning multiple scales, taxa, and environments. 🦠🌎
journals.asm.org/doi/10.1128/...

‘We can change diet to generate a healthier microbiome and a healthy individual’ Microbiologists Justin and Erica Sonnenburg are working to understand the complex microbial community that resides within the human gut and its potential for helping people live healthier, longer live...

From 2 of my favorite scientists:
“We are deeply concerned about the current funding climate. When we think about new professors or postdocs starting their own labs, we worry that funding challenges could easily result in losing a generation of talented scientists.”
news.stanford.edu/stories/2025...

Do people in the same household share strains when they have the same species?

How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?

We answer these and related questions for the facial skin microbiome in our latest paper.

🧵[1/10]

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@wakeforest.bsky.social

I'll take your re-tweets over fancy journal citations any day

Your stomach bacteria is changing the way you think. The saying “thinking with your gut” is more accurate than you probably realize.

...Way ahead of you, Steve-o (from way back in 2014!)

Moral enhancements and your microbiome:
medium.com/gut-check/gu...

Sorry, I'm just reading this now. But are you saying that these investigators reached the wrong conclusion, or that this paper shows that they would have reached the wrong conclusion if they hadn't binned correctly? If the former, whats the evidence that it was wrong?

Removal of sequencing adapter contamination improves microbial genome databases - BMC Genomics Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbi...

Related: We found some MAG databases are contaminated by sequencing adapters, but the collective response was basically "meh..."
link.springer.com/article/10.1...

This is such a great question! Although I think the expectation for even uncovering those mislead conclusions should be scaled to how few people actually look at this.