We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project? That question sent us down a rabbit hole. Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles. 1/3

New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/08/m... • oral-gut microbiome in stunted children / @yersim.bsky.social • female urinary microbiome / @mikeneugent.bsky.social • holobiont / @jake1.bsky.social • invitation for the #MVIF 49 / @microbiomevif.bsky.social & more.

May 8, 2026

See you next week at MVIF! Gut microbiome Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults – Thomas Kar…

microbiomedigest.com

We are delighted to share our vision in #RSCChemBioy of how to incorporate natural product discovery (and any drug discovery) into the framework of personalized medicine - drug discovery using patients, but not in patients! #natprod #secmet pubs.rsc.org/en/content/a...

Did it work? 🤷🏽 But its pretty

I’m thrilled to announce that the Neugent Lab will officially set sail on May 1st, 2026 in the Department of Urology at the University of Rochester Medical Center! My lab will investigate how we can manipulate the ecosystem of host / #microbiome interfaces to impact urologic health.

I’m thrilled to announce that the Neugent Lab will officially set sail on May 1st, 2026 in the Department of Urology at the University of Rochester Medical Center! My lab will investigate how we can manipulate the ecosystem of host / #microbiome interfaces to impact urologic health.

(BioRxiv All) Sodium ion-assisted structural lipidomics for sphingolipid profiling: Sphingolipids are diverse lipids with sphingobases and N-acyl fatty acids as the hydrophobic moieties. While the importance of the in-depth elucidation of hydrophobic structures is widely… #BioRxiv #MassSpecRSS

Sodium ion-assisted structural lipidomics for sphingolipid profiling

Sphingolipids are diverse lipids with sphingobases and N-acyl fatty acids as the hydrophobic moieties. While the importance of the in-depth elucidation of hydrophobic structures is widely recognized in lipid biology, mass spectrometry-based annotation of ceramides in the commonly used protonated form is often hindered by in-source dehydration during electrospray ionization in the heated state and variable water losses in the product ion spectrum. In this study, we investigated the sodium ion form and its product ions in ceramides with the use of electron-activated dissociation tandem mass spectrometry (EAD MS/MS) in addition to collision-induced dissociation to facilitate in-depth structural elucidation. While dehydrated ions from the protonated form were frequently observed, the sodium adduct ions remained stable because of their higher activation energy compared with the protonated form, which was validated using quantum chemical calculations. Using the three adduct forms under optimized conditions increased confidence in annotating the ceramide peaks through retention-time matching. Furthermore, EAD MS/MS of the sodium adduct ions facilitated the positional determination of double bonds and hydroxyl groups in the ceramide hydrophobic moiety. Our approach is showcased by the annotation of phytoceramides with N-acyl 2- and 3-hydroxyl groups in mouse feces and ceramides with N-acyl n-6 very long-chain polyunsaturated 2-hydroxy fatty acids in mouse testis.

dlvr.it

If you’re interested in host–microbe interactions, immunometabolism, mucosal biology, or fungal pathogenesis, I hope you’ll check out the full article. 👇 @science.org www.science.org/doi/10.1126/...

Fungal infection drives metabolic reprogramming in epithelial cells via aerobic glycolysis and an alternative TCA cycle shunt

Candida hijacks epithelial metabolism via glycolysis and GOT1-dependent TCA shunt, influencing antifungal defense.

science.org

Join #MVIF 44 cassyni.com/s/mvif-44 and #MeetTheSpeakers 🇺🇸 Vanessa Hale will discuss technical challenges of low microbial biomass and high host cell shedding in metagenomics analysis of urine samples. Check out the paper: microbiomejournal.biomedcentral.com/articles/10....

Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography https://www.biorxiv.org/content/10.1101/2025.11.30.691379v1

Thrilled to share that our recent work is out in npj Biofilms and Microbiomes. 🧵 (1/4) www.nature.com/articles/s41...

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection - npj Biofilms and Microbiomes

npj Biofilms and Microbiomes - Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection

nature.com

Thrilled to share that our recent work is out in npj Biofilms and Microbiomes. 🧵 (1/4) www.nature.com/articles/s41...

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection - npj Biofilms and Microbiomes

npj Biofilms and Microbiomes - Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection

nature.com

My first author paper is out on JU Open Plus.Check it out! Bladder Wall–Embedded Bacteria Associated With Increased... : JU Open Plus journals.lww.com/juop/fulltex...

Bladder Wall–Embedded Bacteria Associated With Increased... : JU Open Plus

eria within the bladder walls of women with rUTI. We hypothesized that increased bladder wall bacterial burden may be associated with incomplete rUTI resolution after EF. Materials and Methods: Aft...

journals.lww.com

What are we not seeing in the microbiome? 🤔 Metagenomics tells us who’s there—but not what surrounds them. That’s a huge blind spot in microbial ecology. Let me explain. 🧵

🚨 Preprint update Excited to share our updated preprint on the biochemical ecology of recurrent UTI. 🧬 #Metagenomics + #metabolomics 🧪 Lipid biomarkers for active UTI (AUC = 0.91) ⚠️ DCA as a predictor of recurrence 🔗 doi.org/10.1101/2024... #UTI #Microbiome #Metabolomics #PrecisionMedicine

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection

Recurrent urinary tract infections (rUTIs) are a major clinical challenge and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the...

doi.org

TODAY Are you interested in learning more about the urobiome? Join the CAIRIBU U-RIG Research Hour to hear talks from Seth Reasoner, titled "Pathogen Evolution in Neurogenic Bladder" and Katy Patras, titled "The Vaginal Microbiota and Colonization by Uropathogens."

NEXT MONTH Join Urobiome 2025 on February 24th, 2025 in San Diego, CA. Learn more about the state of urobiome research from expert investigators! More information HERE: https://buff.ly/3PHUl0W

THIS WEEK Are you interested in learning about transitional care? Join this CAIRIBU Catalyst Conversation to hear from Dr. Kristin Ebert. Her talk is titled "Navigating the Journey: Enhancing Transitional Care for Urology Patients." More info: https://buff.ly/3Wtazij

Don't forget to submit an abstract to the 10th Annual Duke University Multidisciplinary Benign Urology Research Symposium before the deadline on March 4th! Submit here: https://buff.ly/4ggUSSc

This is amazing!!!! Congratulations!!!! news.utdallas.edu/alumni/howar...

Pain Scientist Earns Howard Hughes Medical Institute Fellowship

Juliet Mwirigi BS’18, PhD’23, who specializes in pain studies, has been selected for a Hanna H. Gray Fellowship. Each of the 25 fellows receives up to $1.5 million in funding over eight years. After a...

news.utdallas.edu

I introduce to you Dr. Molina!!! Congratulations Jon!! You did a great job!!

The GLP-1 family of drugs have anti-inflammatory effects independent of weight loss. 2 new studies shed light on the mechanisms —brain-gut-GLP axis blocks inflammation induced by TLRs (toll-like receptor) www.cell.com/cell-metabol...

Harvard scientists are leaving academia for the private sector to fast-track biomedical breakthroughs. Michael Mina (eMed), Douglas Melton (Vertex), Stuart Schreiber (Arena Bioworks) cite funding delays & admin hurdles as key reasons. #BiomedicalResearch www.harvardmagazine.com/2025/01/harv...

Harvard Professors Leaving for Private Sector Research | Harvard Magazine

Three distinguished scientists on leaving academia to advance biomedical research

harvardmagazine.com

I was today years old when i learned about the mixOmics R package… omg

so proud of Adwaita Parab and Arnold Salazar Baylor College of Medicine presenting their work on #Bladder #organoids #ifrd1 #bladderProteostasis

must mention that our dinner at Zarletti Milwaukee was fantastic 😋

Outstanding annual #CAIRIBU meeting in #MilwaukeeWI. excellent Basic, Translational, and Clinical Sciences research in #Urology #Urogynecology #bladder health #Aging #bladder #Immunology

Good morning, @mikeneugent.bsky.social! (A year ago, Mike and I started spontaneously our coffee greeting thread on X, and, obviously now we are transferring it here)

Where did November go?

Hey #metabolomics friends! What is your favorite open-source tool for deconvoluting Waters MSe data?