Travis Gibson

A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

Attomolar fecal cytokine profiling reveals gut immune dynamics and disease states https://www.biorxiv.org/content/10.64898/2026.03.31.714463v1

It's time for the 2025 Gibbons Lab Research Roundup! Yeehaw! 🤠 @isbscience.org In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️‍🩹 🧵...

If you missed the 2025 @isbscience.org Virtual Microbiome Symposium (theme: how microbial metabolites influence the brain, the immune system, & metabolism), the videos of the talks and the panel discussion are now available here: youtube.com/playlist?lis... Thanks to all who helped make it happen!

You still have time to register for our @isbscience.org Virtual Microbiome Symposium (Dec. 12th), with 6 speakers discussing how microbial metabolites impact the nervous, immune, and endocrine systems. It's free! Recordings of the talks will be available afterwards. isbscience.org/events/2025-...

#Newresearch This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice. #MicroSky www.nature.com/articles/s41...

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

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...

Im working on something and I am reminded of one of the wildest correspondences ever published www.nature.com/articles/nbt...

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

Our paper is now open access as well.

New paper in Genome Biology! genomebiology.biomedcentral.com/articles/10.... We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).

This month's editorial is an invitation to submit papers on clinical and translational aspect of the microbiome. This collection is a joint effort with @naturemedicine.bsky.social @natcomms.nature.com and @commsbio.nature.com #MicroSky #MicrobiomeSky 🦠⚕️🧪⚕️ www.nature.com/articles/s41...

🚨 Out now! Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻 @travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org #MicroSky 🦠 #MicrobiomeSky www.nature.com/articles/s41...

"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al. rdcu.be/ekTwf

It is a great pleasure to listen to @seppekuehnlab.bsky.social His talk is about ´Learning microbiome design principles from natural variation ´. Below, the #liveSketch painting during the seminar and given at the end! #ArtAndScience #MediationScientifique

Several Postdoctoral Fellow openings. All fellows have triple appointment at HMS,BWH, and Broad - Biological sequence models (theory, design, and application) - Learning single cell dynamics - Bacteriotherapy design, “bugs-as-drugs” (using control theory principles) gibsonlab.io/openings/

We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.

A must-read for any microbiome researcher 🦠📐and a new addition to our #bestpractices series Planning and describing a microbiome data analysis by @amydwillis.bsky.social and @davidandacat.bsky.social www.nature.com/articles/s41...

Paper just accepted Gibson et al. "On the stability of gradient descent with second order dynamics for time-varying cost functions" Transactions Machine Learning Research (2025) openreview.net/forum?id=Hlz...

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...

Join us in LA this March!

Are regret based adaptive control strategies deployable? arxiv.org/abs/2501.04572

This post has saved hours when trying to get old x86 bioinformatics pipelines working on Mac arm64 (like pplacer) stackoverflow.com/questions/64...

It’s easy to think this is about politics, but Ran’s actually just subtweeting my working style

When can a sum of reciprocals of natural numbers sum to a rational number? There are many unsolved problems in this area, by Erdős and others. With Vjeko Kovac, we have been able to resolve some open questions and make progress on others: terrytao.wordpress.com/2024/11/27/o...

Congrats Robert

Retraction Note: Culture of previously uncultured members of the human gut microbiota by culturomics | Nature Microbiology www.nature.com/articles/s41...

Ok this is really cool. Using the lab website I can have the lab handle: @gibsonlab.io my handle: @travis.gibsonlab.io

@baym.lol are you doing in evolutionary studies with hCom2?

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

Happening in 20 Minutes this talk will cover their EVO model which was published in Science this week and made the cover

Monday at 4pm EST on Zoom. All info in link Brian Hie - Stanford “Sequence modeling from molecular to genome scale with Evo” comp-path.bwh.harvard.edu/events-all/b...

Most recent work out of joint NSF project with Wang-Gerber-Gibson labs. First author Guillaume Urtecho just started his own group at UCSD! "Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut" free-access link authors.elsevier.com/c/1k5Yh8YyDf...