iiinova — where your digital self keeps evolving

Reposted by Tim Straub

Nature Portfolio @natureportfolio.nature.com · 24/05/2026

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

Evolution of next-generation probiotics therapy

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Tim Straub @timothystraub.com · 07/03/2026

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

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Tim Straub @timothystraub.com · 05/03/2026

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.

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Reposted by Tim Straub

Pieter Dorrestein @pieterdorrestein.bsky.social · 05/03/2026

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

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Reposted by Tim Straub

APC Microbiome Ireland @apcmicrobiomeirel.bsky.social · 24/02/2026

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 ⬇️

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.

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Tim Straub @timothystraub.com · 21/02/2026

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!

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Tim Straub @timothystraub.com · 13/02/2026

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

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Reposted by Tim Straub

Nature Portfolio @natureportfolio.nature.com · 30/01/2026

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 🧪

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

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Tim Straub @timothystraub.com · 24/01/2026

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/

tstraub89.github.io

gallery_wall

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Tim Straub @timothystraub.com · 06/01/2026

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...

nature.com

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...

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Reposted by Tim Straub

Stephen Turner @stephenturner.us · 21/11/2025

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

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Reposted by Tim Straub

Johns Hopkins Berman Institute of Bioethics @bermaninstitute.bsky.social · 13/11/2025

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...

science.org

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

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Reposted by Tim Straub

Erik Bakkeren @erikbakkeren.bsky.social · 07/11/2025

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...

nature.com

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.

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Tim Straub @timothystraub.com · 14/10/2025

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

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Tim Straub @timothystraub.com · 10/10/2025

👀 What an interesting and under-explored idea!

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Reposted by Tim Straub

Microbiome Virtual International Forum @microbiomevif.bsky.social · 10/10/2025

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...

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Reposted by Tim Straub

Elaine Hsiao @pipethero.bsky.social · 25/09/2025

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!

rdcu.be

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...

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Tim Straub @timothystraub.com · 19/09/2025

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

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Reposted by Tim Straub

Tami Lieberman @contaminatedsci.bsky.social · 12/09/2025

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.

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Tim Straub @timothystraub.com · 12/09/2025

🧬 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)!

tinyhealth.com

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...

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Tim Straub @timothystraub.com · 10/09/2025

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.

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Reposted by Tim Straub

Titus Brown @titus.idyll.org · 08/09/2025

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!

pubmed.ncbi.nlm.nih.gov

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...

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Reposted by Tim Straub

Nature Portfolio @natureportfolio.nature.com · 06/09/2025

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 🧪

go.nature.com

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.

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Tim Straub @timothystraub.com · 31/08/2025

Just came across this preprint: groups at @broadinstitute.org and MGH developed a low-cost, #CRISPR based diagnostic for pathogenic bacteria and #AMR genes from blood cultures.

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Tim Straub @timothystraub.com · 29/08/2025

This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

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Reposted by Tim Straub

Hatzios Lab @hatzioslab.bsky.social · 04/08/2025

Congrats to postdoc Zhe Zhou on her paper out today in @cp-cellhostmicrobe.bsky.social showing that gut bacteria cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Thanks to collaborators Angela Jiang and Xiaofang Jiang at NIH. www.sciencedirect.com/science/arti...

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Reposted by Tim Straub

Guillaume Méric @gmeric.bsky.social · 05/08/2025

Is the gut microbiota composition in the 1st week of life linked to viral lower respiratory tract infections (vLRTIs) in early childhood? Here, work using the BBS birth cohort identifies Bifidobacterium longum-dominated cluster linked to lowest vLRTI rates 🔗 www.sciencedirect.com/science/arti...

sciencedirect.com

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics

Early-life gut microbiota affects immune system development, including the lung immune response (gut–lung axis). We aimed to investigate whether gut m…

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Tim Straub @timothystraub.com · 31/07/2025

This study published today finds "a more diverse gut microbiome is generally associated with healthier glucose spike metrics." It's certainly not implying causality, but it is very interesting to see the association!

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Reposted by Tim Straub

Ivan Zanoni @lozanzi.bsky.social · 26/07/2025

#WeekendRead! #EveryCellIsAnImmuneCell! #TollPower! Kaelberer Bohorquez &co show @nature.com that #TLR5 signaling in response to flagellin drives neuropeptide PYY release by gut colonic neuropod cells, activating vagal neurons that signal to #brain, reducing feeding via a “neurobiotic sense”!

nature.com

A gut sense for a microbial pattern regulates feeding - Nature

A study reveals a gut–brain sensory pathway through which the microbial component flagellin activates neuropod cells in the colon to signal the brain and reduce feeding in mice.

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Reposted by Tim Straub

Reiner @erlangen.bsky.social · 05/07/2025

Widespread Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis www.nature.com/articles/s42... Missing beneficial bacteria in infant guts linked to rising asthma and allergy cases medicalxpress.com/news/2025-07... Fecal samples from participants in 48 of 50 US states

nature.com

Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis - Communications Biology

The My Baby Biome Study demonstrates that three gut microbiome community clusters exist in infants in the United States. These compositions vary on the prevalence and abundance of Bifidobacterium and ...

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Reposted by Tim Straub

Sergio Andreu-Sanchez @seandreu.bsky.social · 30/04/2025

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...

sciencedirect.com

Global genetic structure of human gut microbiome species is related to geographic location and host health

The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

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Reposted by Tim Straub

Segata Lab @cibiocm.bsky.social · 18/04/2025

OPEN CALL for PhD positions in our lab through the semm_it program: 1️⃣ Microbiome signatures of early on-set colorectal cancer 2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission More info: www.semm.it/education/op... Apply by June 9!

semm.it

Open Positions | SEMM European School of Molecular Medicine

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Tim Straub @timothystraub.com · 18/04/2025

argNorm looks like a promising tool to analyze antimicrobial resistance genes from metagenomic data. Having tested and benchmarked different ARG databases and software suites in the past, argNorm would have come in handy. #microbiomesky #idsky #AMR

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Reposted by Tim Straub

Food Allergy Science Initiative @foodallergyscience.org · 17/04/2025

Exciting research out of Dan Littman’s group! Dan serves on our SAB. #immunosky #microbiomesky #allergysky #foodallergy

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Reposted by Tim Straub

Sean Gibbons 🦠💩 @gibbological.bsky.social · 11/04/2025

Microbial community-scale metabolic models (MCMMs) map gut microbiome composition & dietary context to functional outputs, at scale. Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com www.nature.com/articles/s41...

nature.com

Moving from genome-scale to community-scale metabolic models for the human gut microbiome - Nature Microbiology

In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

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Tim Straub @timothystraub.com · 12/04/2025

This review touches on a lot of aspects of clinical #microbiome research. Solid read.

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Reposted by Tim Straub

Guillaume Méric @gmeric.bsky.social · 27/03/2025

Nice study showing that 6-wk HAMSAB intervention in adults with T1D impacts gut mucosal immunity & host-microbiome metabolism. Some participants (2 responders/2 non-resp) then used as FMT donors in NOD mice to identify SCFA producers linked to anti-inflam + IgA prod. 🔗 www.nature.com/articles/s41...

nature.com

SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome - Nature Communications

In a previous clinical trial, the authors reported that SCFA-yielding biotherapy in adults with type 1 diabetes remodels the gut proteome and metabolome. Here, the show that colonization of the post-t...

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