Tim Straub
@timothystraub.com
Senior Data Scientist @ Tiny Health Data science | bioinformatics| computational biology Broadly interested in NGS and multi-omics, microbiome, infectious disease, ML/AI, cool science, and big data. Also golden retrievers. All views are my own.
A Review in Nature Reviews Microbiology discusses recent advances in the design of next-generation probiotics and highlights major challenges and the potential of AI to develop effective, personalized probiotics with therapeutic functions. go.nature.com/42L3xYX 🧪 #microbiome
My side project continues to take up my nights and weekends! Lots of cool updates in this version released today. Check it out!
GalleryPlanner@gallery-planner.com · 6mo agoGalleryPlanner v1.1 is now live! Pro passes are now available: 3-day, 7-day, 30-day, and Lifetime Pro. Also in this update: - Pro Export Pack - Better mobile experience - More desktop controls And a revamped landing page --> gallery-planner.com #gallerywall #homedecor #interiordesign #saas
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.
Sean Gibbons 🦠💩@gibbological.bsky.social · 6mo agoVery cool paper www.nature.com/articles/s43... The authors found that FMTs from *older* mice into adult females improved ovarian function and lowered inflammation. FMTs from younger mice into adult mice led to higher inflammation and *reduced* ovarian function in older mice.
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...
biorxiv.org
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!
GalleryPlanner@gallery-planner.com · 6mo ago🎉 GalleryPlanner v1.0 launched today Built out of a need to plan gallery walls without uploading private family photos. Privacy-first features: 🔒 100% local AI processing 📱 Photos never leave your device 💾 No cloud storage, no uploads Try it free → galleryplanner.com
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
GalleryPlanner@gallery-planner.com · 6mo agoPlanning a gallery wall with tape + guesswork is brutal. Gallery Planner Pro (free in beta) gives you: - Smart layout suggestions for your frames - AI‑assisted photo selection - Printable hanging guides - Cropped high‑res exports ready to print or send to clients Just go to gallery-planner.com
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 🧪
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/
gallery_wall
tstraub89.github.io
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...
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...
nature.com
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.
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....
globenewswire.com
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. | Science | AAAS www.science.org/content/arti...
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.org
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...
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.
nature.com
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
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...
rdcu.be
Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....
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...
microbiomejournal.biomedcentral.com
👀 What an interesting and under-explored idea!
Rachel M. Wheatley@rachelmwheatley.bsky.social · 11mo agoIs a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
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/...
Microbiome and Reproductive Health
Microbiome is calling for submissions to our Collection on Microbiome and Reproductive Health. Our understanding of the intricate relationship between the ...
link.springer.com
Microbiome@microbiomej.bsky.social · 11mo agoIn #Microbiome: 🦠Exploring how the microbiome influences fertility & preconception health 🚨Offering a systems-level lens through which to understand & improve reproductive health by linking diet, immunity, metabolism & hormonal signaling Read more👉 doi.org/p7cw
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!
Complex carbohydrate utilization by gut bacteria modulates host food consumption
Nature Communications - Gut bacteria digest dietary fiber and release molecules as energy for the host. Here, Yu et al. find that the ability of certain gut bacteria to digest different fibers...
rdcu.be
Elaine Hsiao@pipethero.bsky.social · 3y agoDelighted to share work by Kristie Yu, Celine Son, & co showing that selective fructan metabolism by the gut microbiome can contribute to host associative learning of dietary preference, even when it comes to choosing between diets with the same perceptual salience (and macronutrient composition!)
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
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...
doi.org
👀 This looks really interesting–being able to understand genomic context and assess species carriage of #ARGs from WMS data. #microbiome
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo agoCARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences https://www.biorxiv.org/content/10.1101/2025.09.15.676352v1
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.
🧬 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)!
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...
tinyhealth.com
MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes genomebiology.biomedcentral.com/articles/10.... #jcampubs
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...
genomebiology.biomedcentral.com
Authors argue that integrating metagenomics, culturing, and experimental validation to study hidden yet ecologically significant microbial species will advance our understanding of the microbiome in health and disease, and inform next-gen therapeutics leveraging the full diversity of the gut.
Alexandre Almeida@alexmsalmeida.bsky.social · 12mo ago🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...
There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed
Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...
pubmed.ncbi.nlm.nih.gov
A Nature Outlook article reports on the preliminary evidence that microbiota-based treatments can be beneficial for people with mood disorders, such as depression and anxiety. But how these interventions work is not clear, and human trials are needed. #microbiome #medsky 🧪
Why nurturing the gut microbiota could resolve depression and anxiety
Links between gut microbes and mental health could lead to large-scale trials of probiotic interventions.
go.nature.com
1/3 🧬 Exciting news from my colleagues at Tiny Health! New study: A personalized #microbiome program helped C-section babies develop more normal gut microbiomes AND showed 83% lower odds of atopic dermatitis!
Improving immune‐related health outcomes post‐cesarean birth with a gut microbiome‐based program: A randomized controlled trial
Background Infants born via Cesarean section (C-section) often have a distinct gut microbiome and higher risks of atopic and immune-related conditions than vaginally delivered infants. We evaluated ...
onlinelibrary.wiley.com