Interested in a *staff computational scientist* position? We are looking for an experienced computational biologist (ideally with microbiology experience) to support published packages while also driving new research. Pay range $73k-$111k w excellent benefits. careers.peopleclick.com/careerscp/cl...
REMINDER - Abstract submission deadline for MEEHubs2026 is April 19! Get you abstract in and present at one of the hubs August 3-5, 2026✨You'll be in great company! We have a fantastic lineup of speakers‼️
Links and more info here: meehubs.org
I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)
Image of the cover of the 1st volume of ISME Host Microbe a new official journal of the International Society for Microbial Ecology. Cover images shows a plant stomata with bacteria around and entering.
Excited to announce our new journal from @isme-microbes.bsky.social ISME Host Microbe is live and now accepting submissions. Look forward to receiving your papers! #Microsky 🧫 🦠
If I had only realized that my kids were running experiments all weekend!
"Microbiota transfers were performed with repeated seeding of forest soil onto rugs placed in the home entryway."
link.springer.com/article/10.1...
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.
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).
I think everyone can relate to the importance of science for healthcare, and I’ve been sharing these slides for people to use and adapt with their own stories! youtu.be/BY_SFgi-Cig
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
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
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
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.
Check out this incredible analysis!
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...
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
#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.
🔬 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/...
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]
This is exciting! Top reporting on Science, Biotech, Health Policy, and Public Health news.
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