My side project continues to take up my nights and weekends! Lots of cool updates in this version released today. Check it out!

Cool mouse model showing how the gut microbiome is so personalized! A healthy microbiome is NOT one size fits all. Bugs and host are likely co-adapting as we age.

Yet another new function of bile acids -and relevance of the microbiome in regulating the efficacy of medications.
#microbiome #IBD. Discovered using #metabolomics repository scale analysis.
#opendata Thanks to all the collaborators and Vincent for leading it. www.biorxiv.org/content/10.6...

An unhealthy diet disrupts feeding behavior and the gut microbiota, but whether early-life dietary effects persist, or can be restored later in life, remains unclear. We investigated whether microbiota-targeted interventions (FOS + GOS or Bifidobacterium longum APC1472) could restore early-life highfat/ high-sugar (HFHS) diet-induced feeding alterations in adult female and male mice.

New APC paper in Nature Comms
First author Cristina Cuesta-Marti and colleagues examine how eating unhealthy foods early in life leaves lasting brain and feeding changes but bacteria can help restore healthy eating.

www.nature.com/articles/s41...
#Microbiome #GutBrainAxis
Tagging collaborators ⬇️

My nights and weekends have been busy working on this passion project: #GalleryPlanner. It’s my first foray into #SaaS and #FrontEnd #WebDev. Check it out!

My side project has its own account now! So I'll keep posting about the #microbiome and #science here, but follow @gallery-planner.com for tips and tricks 🎨🖼️

#sideproject #gallerywall #galleryplanner

This is figure 4, which shows function and disease association of microbially targeted human proteins.

Analyses published in Nature Microbiology identify commensal type III secretion systems and substrates in the human gut #microbiome that can interact with human proteins to modulate immune pathways. go.nature.com/4tdojfU 🧪

A good reminder how the same skills I use for work–problem framing, data structure design, iterative experimentation–translate directly to home projects. Started with "what do I actually have (frames, photos, wall space)" and built from constraints up. Works for microbiome data, works for walls.

GitHub - tstraub89/gallery_wall: A web app for designing and organizing gallery walls A web app for designing and organizing gallery walls - tstraub89/gallery_wall

Features: drag-and-drop photos into frames, staircase templates, circular/oval frames, export print-ready crops. Plus a text-based frame importer that parses simple text files into actual frames.

GitHub repo: github.com/tstraub89/ga...

I built a gallery wall planner because I couldn't find one that handled real frame inventory + placing actual photos. I'm a data scientist, not a front-end dev. I had no idea what React was, but I vibe-coded it with Gemini + Antigravity IDE over a few weekends.

tstraub89.github.io/gallery_wall/

This work shows that precision microbiome-based therapies like VOWST can durably restore colonization resistance, shifting rCDI care beyond repeated antibiotics toward short-course, mechanism-driven treatment that rebuilds a resilient gut ecosystem.

We found:
- High-dose VOWST enabled rapid, durable engraftment and rescued efficacy in phase 3 vs phase 2
- VOWST shifted the gut toward a healthy-like community, reducing Proteobacteria and C. diff
- Engrafted Firmicutes restored key metabolites (secondary bile acids, SCFAs) that inhibit C. diff

The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome - Nature Medicine An exploratory analysis of the phase 3 ECOSPOR III trial shows that a higher dosage of the oral microbiome therapeutic VOWST led to enhanced pharmacokinetics, increased species engraftment and altered...

It's finally out today in Nature Medicine - a huge shout out to Jess Bryant and the entire Seres team, past and present, on this post hoc analysis of microbiome omics data across all three clinical trials of VOWST (aka SER-109).

Read it here:
www.nature.com/articles/s41...

Find more info on how to participate here: www.tinyhealth.com/research/ora...

Tiny Health and Bristle Health Launch Groundbreaking Study on Oral-Gut Health Connection Tiny Health and Bristle Health recruit participants for pioneering research on the oral–gut microbiome connection and digestive health....

Check out the latest research edition from Tiny Health (my company) looking at the oral-gut axis, partnering with Bristle Health to simultaneously test your oral and gut microbiomes.

Review: Evaluation of metagenome binning: advances and challenges academic.oup.com/bib/article/... 🧬🖥️🧪

Research linking gut microbes to autism is deeply flawed, critics say Amid growing investment in the field, a new paper argues it rests on shaky foundations

Research linking gut microbes to autism is deeply flawed, critics say. Amid growing investment in the field, a new paper argues it rests on shaky foundations. | Science | AAAS www.science.org/content/arti...

Strain displacement in microbiomes via ecological competition - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social

rdcu.be/eMmcT

Distinguishing diet- and microbe-derived metabolites in the human gut - Microbiome Background Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbio...

Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....

I welcome another promising tool to analyze strain-resolved WMS data! #microbiome

👀 What an interesting and under-explored idea!

illumina mvif webinar

SAVE THE DATE: 27 October, 2025
and join speakers from both illumina and #MVIF!

Registration for the webinar is free: emea.illumina.com/events/webin...

👀 One of the first two articles published for the collection on #Microbiome and Reproductive Health!

link.springer.com/collections/...

Happy to share this paper in final form rdcu.be/eH8tj, with more info on neuronal responses and potential mechanism of actions! The results suggest that there is neural interoception of microbial metabolic state 🧠🦠 We hope they can inspire more work in this area!

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks

👀 This looks really interesting–being able to understand genomic context and assess species carriage of #ARGs from WMS data. #microbiome

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

Enter Tiny Health's 30 Plants Challenge for your chance to win big Join Tiny Health’s free 7-day gut health challenge and get expert tips, daily inspiration, and recipes to help you reach 30 different plants and a healthier gut. Why 30? Research shows that eating a w...

🧬 Research from the American Gut Project shows that people who eat 30+ different plants per week tend to have a more diverse gut #microbiome than those eating under 10.
At Tiny Health, we're running a fun 7-day challenge to help you get there—plus one winner gets a gut health test ($199 value)!

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes - Genome Biology Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG databa...

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes genomebiology.biomedcentral.com/articles/10.... #jcampubs