New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8
Rita Oliveira
@aritaoliveira.bsky.social
Postdoc @ Duchossois Family Institute @ UChicago Pamer Lab. PhD Alumni @ IGCiencia #gut #microbiome #consortia #diet #machinelearning #Klebsiella
A strict “gatekeeper” decides whether a #fecaltransplant is effective: sohub.io/wruy. This is shown by a new study led by @bahtiyil.bsky.social from #unibern & @inselgruppe.bsky.social @dbmr-unibe.bsky.social
A stool transplant delivers billions of microbes into a sick gut. Almost none move in for good. We followed donor-recipient pairs from whole communities down to single nucleotides, and found the gut runs a ruthless strain-level filter. Out now in Cell Reports 🧵 www.cell.com/cell-reports...
Strain-level ecological filtering governs microbial colonization of the human gut
Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...
cell.com
Universität Bern@unibe.ch · 3mo agoA strict “gatekeeper” decides whether a #fecaltransplant is effective: sohub.io/wruy. This is shown by a new study led by @bahtiyil.bsky.social from #unibern & @inselgruppe.bsky.social @dbmr-unibe.bsky.social
Thrilled to share that our new paper is out now in @natcomms.nature.com 🎉 Huge congrats to @vhrcabral.bsky.social and @karinaxavierlab.bsky.social on this major work. We found that our Klebsiella ARO112 can break the antibiotic/inflammation cycle in an IBD model
Klebsiella ARO112 promotes microbiota recovery, pathobiont clearance and prevents inflammation in IBD mice
Nature Communications - Here, the authors provide evidence of the biotherapeutic potential of Klebsiella ARO112 for gut inflammatory conditions by showing it accelerates pathobiont clearance and...
urldefense.com
Revised preprint is online 📖 What's new? -2nd probiotic intervention trial showing accurate engraftment predictions -Akkermansia growth rates associated with lower glucose AUC -Longitudinal improvements in metabolism associated with MCMM-predicted butyrate flux www.medrxiv.org/content/10.1...
Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across two human intervention trials.
Prebiotic, probiotic, and combined (synbiotic) interventions often show variable outcomes across individuals, driven by complex interactions between introduced biotics, the endogenous microbiota, and ...
medrxiv.org
Sean Gibbons 🦠💩@gibbological.bsky.social · last yr.Our latest preprint is online @medrxivpreprint.bsky.social: "Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial." www.medrxiv.org/content/10.1... Amazing work here by postdoc Nick Quinn-Bohmann @isbscience.org 🧵...
A diet enriched in microbiome-fermentable substrates (more fruits and veggies) was shown to be associated with lower frailty and lower mortality risk in an older cohort (N>6000; 65+ y/o), with inflammation markers significantly mediating the dietary effect. link.springer.com/article/10.1...
Associations of dietary intake for gut microbiota with frailty risk and mortality in older adults - Journal of Translational Medicine
Journal of Translational Medicine - The associations between a diet that associated with a healthy gut microbiota and the risk of frailty, as well as mortality in older adults with frailty, remains...
link.springer.com
Excited to share new work by Guli Agirman + co that identifies a direct mechanism linking gut microbial imidazole propionate to stress! 🧠🦠 Btw this image was made by Nano Banana Pro 🍌. First time I've gotten a model to accurately generate a science graphic 🤯 authors.elsevier.com/a/1mA5M6t8JE...
Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis in #mSystems from Margaret McFall-Ngai journals.asm.org/doi/10.1128/...
Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis | mSystems
Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of...
journals.asm.org
Today we announce the launch of the MICROBIOME MEDAL, an annual recognition that embodies our commitment @psumbiome.bsky.social to honor a singular scholar or group of scholars who nobly extend excellence, acumen, and ingenuity in the microbiome sciences worldwide. www.psu.edu/news/huck-in...
Host-microbiome interaction biologist to receive inaugural Microbiome Medal | Penn State University
The One Health Microbiome Center will present the inaugural Microbiome Medal to Thomas Bosch on Dec 12. Bosch, a developmental biologist, zoologist and distinguished senior professor at Kiel Universit...
psu.edu
#NewResearch A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated C. difficile infection in mice. #MicroSky 🦠💊 www.nature.com/articles/s41...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology
A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.
nature.com
New in Nat Comm Pathogenic E. coli use protein FimH to grab onto the gut lining New microgels mimic the mannose binding sites—acting as “decoys” to drag bacteria away and protect the intestine in IBD Adherent-invasive E. coli (AIEC), enriched in Crohn’s disease, are a key target for this strategy
Fishing out AIEC with FimH capturing microgels for inflammatory bowel disease treatment - Nature Communications
Inflammatory bowel disease (IBD) is a chronic immune-mediated condition. This study presents a drug-free treatment strategy for IBD that targets bacterial adhesion, utilizing mannan oligosaccharide-lo...
nature.com
If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...
cell.com
Delighted to announce the @keystonesymposia.bsky.social meeting: Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection. Join us in Breckenridge in May 2026!! You can check out the program and amazing lineup of speakers below: keysym.us/KSAntibiotics26 #KSAntibiotics26
Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia
Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!
keysym.us
Why are certain vancomycin-resistant Enterococcus (VRE) strains taking over hospitals? Emergent lineages make bacteriocin T8—giving them a gut colonization edge over older strains Microbial competition shapes nosocomial evolution Mills et al Nat Microbiol #VRE #AMR www.nature.com/articles/s41...
Read our latest #perspective on small intestinal microbiota, published with @SpringerNature in @NatRevGastroHep. #GutMicrobiota #MicrobiomeScience #Smallintestine Perspective👉 rdcu.be/dXQ6y
Delving the depths of ‘terra incognita’ in the human intestine — the small intestinal microbiota
Nature Reviews Gastroenterology & Hepatology - The small intestinal microbiota has a key influence on digestion, immunity and nutrient metabolism but is poorly understood in comparison with the...
rdcu.be
Free access to 2,656 metabolites from 9 platforms measured at 56 time points and covering 6 challenges "suffered" by 15 healthy volunteers: The HuMet Repository - Watching human metabolism at work www.sciencedirect.com/science/arti... All data provided in an interactive repository: humet.org
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:
Metagenomic estimation of dietary intake from human stool - Nature Metabolism
Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.
nature.com
A link between yogurt intake and reduce risk of colon cancer, from cohort of over 130,00 participants, with inverse relationship to Bifidobacterium in gut microbiome www.tandfonline.com/doi/full/10.... open-access
Scripps Research awards 2024 Collaborative Innovation Fund grants to three teams pioneering high-risk, high-reward research. Projects include next-gen antibiotics to combat superbugs, rewiring protein interactions for new therapies, and advancing safer genome editing.
Collaboration awards enable scientists to design new medicines, more precisely edit DNA and fight drug-resistant bacteria
scripps.edu
OUT NOW: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome @harriswang.bsky.social & co www.nature.com/articles/s41...
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology
Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.
nature.com
Our technique for studying strain-level IgA binding in the microbiome is out now at @naturemicrobiol.bsky.social! Fascinated by IgA since Sean Spencer told me about it, here we make some fundamental discoveries about strain-level IgA dynamics in the healthy human gut (1/5) doi.org/10.1038/s415...
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
doi.org
We showed that #metaproteomics based "Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switching in vivo" www.biorxiv.org/content/10.1... Great work by Angie Mordant and Alfredo Blakeley-Ruiz @alfredob.bsky.social
Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switching in vivo
Diet has strong impacts on the composition and function of the gut microbiota with implications for host health. Therefore, it is critical to identify the dietary components that support growth of spe...
biorxiv.org
At npjAMR we are looking for an early career researcher to take on a dual role of Social Media Editor and Trainee Associate Editor. Lots of training and support provided to develop skills in editing. Details, contact info and how to apply in the link below.Pls repost! www.nature.com/npjamar/edit...
Call for Applications: Social Media & Trainee Associate Editor | npj Antimicrobials and Resistance
Call for Applications: Social Media & Trainee Associate Editor
nature.com
Infection and Immunity has a call for papers on Women’s Health and the Development of Microbiota in Childhood. For details see journals.asm.org/journal/iai/...
Women’s Health and the Development of Microbiota in Childhood
Explore expert research on women’s health and microbiota development in children
journals.asm.org
How does the immune system make "decisions" at mucosal barriers? My new perspective explores how seeing strategic cell interactions through the lens of game theory could reveal fresh insights into mucosal immune homeostasis and disease. 🧵 1/7 www.sciencedirect.com/science/arti...
Organismal mucosal immunology: A perspective through the eyes of game theory
In complex organisms, functional units must interact cohesively to maintain homeostasis, especially within mucosal barriers that house diverse, specia…
sciencedirect.com
Quite a comprehensive piece of work: "Gut physiology and environment explain variations in human gut microbiome composition and metabolism." www.nature.com/articles/s41... Definitely worth checking out if you work on animal microbiomes, especially in the gut
Gut physiology and environment explain variations in human gut microbiome composition and metabolism - Nature Microbiology
An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.
nature.com
Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. A study in Nature Microbiology presents an approach to systematically discover and understand such antibiotic relationships. https://go.nature.com/49of3Mk 🧪
📖 New paper from the Pamer lab! Qiwen Dong and collaborators showed that the avirulent C. difficile isolate ST1-75 outcompetes virulent C. difficile to protect mice from colitis, likely by depleting amino acids. ST1-75 has biotherapeutic potential for recurrent CDI! www.cell.com/cell-host-mi...
Protection against Clostridioides difficile disease by a naturally avirulent strain
Dong et al. show that the avirulent C. difficile isolate ST1-75 outcompetes virulent C. difficile strains to protect mice from colitis, likely by depleting amino acids more efficiently. Because ST1-75 has a competitive advantage during coinfection, it has high biotherapeutic potential for preventing and treating recurrent C. difficile infections.
cell.com