Connor Tiffany
@microbe-enjoyer.bsky.social
Post Doc exploring the early life gut microbiome in the Zackular lab @ChildrensPhila. Sometimes develops R packages and shiny apps.
13. Hence our dismal conclusion: rather than finding that LLMs free us to do a better job of what we were doing before they came along, they shift scientific incentives (and the playing field of academic competition) in ways that compel us to do more and more, faster and faster, less and less well.
How does the early life microbiota protect the infant against excessive adiposity? Our new preprint describes a mechanism by which specific members of the early life small intestine microbiota regulate intestinal epithelium-immune interactions to prevent adiposity. www.biorxiv.org/content/10.6...
Small intestine microbiota development prevents early-life adiposity via IL-22-mediated intestinal PPARα suppression
Perturbation to the early-life microbiota has long-term detrimental effects on health and development, leading to increased risk for metabolic dysfunction and childhood obesity. Despite the central ro...
biorxiv.org
We found maternal helminth infection can promote antiviral immunity in offspring 🤱🪱 www.cell.com/cell-host-mi... Don’t worry, we are not suggesting we reinfect everyone with worms! Instead, we identified a microbiota-derived metabolite, Indole-3-propionic acid, that enhances antiviral immunity!
Maternal helminths rewire the microbiota to promote offspring antiviral immunity
Fernandes et al. show that maternal helminths, long-standing mammalian partners, confer antiviral immunity to offspring via the microbiota-derived metabolite indole-3-propionic acid (IPA). This work r...
cell.com
Why has the #Salmonella ST34 become a global pandemic clone? The answer is in the #pig gut—and our use of #copper. Our latest research dives into the "copper-modified niche" and how it reshapes the microbiome. link.springer.com/article/10.1... @rafalkolenda.bsky.social @abaumler.bsky.social
Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium - Microbiome
Background Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimuri...
link.springer.com
Very excited to share our new work from previous Byndloss Lab grad student @shealynicg.bsky.social published today! journals.asm.org/doi/10.1128/...
Aspartate aminotransferase is required for Salmonella expansion in the inflamed gut via TCA anaplerosis | Infection and Immunity
Despite being the primary site of digestion, the mammalian gut represents a region of nutrient scarcity for potential invading enteric pathogens such as Salmonella enterica serovar Typhimurium (S. Tm)...
journals.asm.org
Happy to share this study from the lab led by Orlaith Keenan published in mBio! Working with an outstanding collaborative team, Orlaith demonstrated that maintaining the right balance of neutrophils is key to limiting severe disease during C. difficile infection. journals.asm.org/doi/10.1128/...
Pharmacological reduction of neutrophil infiltration reduces Clostridioides difficile infection severity | mBio
Clostridioides difficile remains a leading cause of antibiotic-associated diarrhea worldwide and a major healthcare burden. While antibiotics are commonly used to treat CDI, high antibiotic resistance...
journals.asm.org
Here we show that buildup of uremic toxins during CKD generates nitrate in the colon. Nitrate supports expansion of Enterobacteriaceae, turning them into a major source of uremic toxins. Inhibiting nitrate production (iNOS inhibition) mitigates disease progression. www.science.org/eprint/YGNMK...
Join us in beautiful Madison WI! In addition to the postdoc call I previously announced, I am seeking applicants for a Scientist position. IMO this position is best suited for someone who successfully completed their postdoctoral training, see here for more details: jobs.wisc.edu/jobs/scienti...
Scientist I – C. difficile and Gut Microbiome - Madison, Wisconsin, United States
Current Employees: If you are currently employed at any of the Universities of Wisconsin, log in to Workday to apply through the internal application process.Job Category:Academic StaffEmployment Type...
jobs.wisc.edu
Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...
Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials
Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...
doi.org
Very cool study and impressive work! Congrats! @qianxuan.bsky.social
Qianxuan(Sean) She@qianxuan.bsky.social · 6mo agoOver 3 years we performed WGS-based surveillance of S. aureus in the NICU at @childrensphila.bsky.social, sequencing both surveillance and bloodstream infection isolates, to understand how colonization, transmission, and persistence are associated with invasive infection in high-risk neonates.
Check out our review on emerging technologies for diet tracking in Nature Food. 👇 This paper was led by @catalinacuparencu.bsky.social, with @cdiener.com and others: www.nature.com/articles/s43... @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social
Integration of modern technologies to advance dietary assessment - Nature Food
Accurately measuring dietary intake has long been a challenge in nutrition research. Integrating emerging tools with multisampling strategies and a dietary assessment methodology aligned with the rese...
nature.com
Center for Microbial Medicine clinicians and researchers team up to tackle bacterial infections in NICUs. Check out the amazing work being done by @pjplanet.bsky.social @ahmedmicrobes.bsky.social Lakshmi Srinivasan and more! @chopresearch.bsky.social www.research.chop.edu/cornerstone-...
The Science Behind the Spread: Researchers Aim to Reduce Bacterial Burden in NICUs
Researchers are using whole genome sequencing techniques to identify possible high-risk strains of bacteria in neonatal intensive care units.
research.chop.edu
Here's a summary of all the data that supports adding more red meat to your diet
As far as I can tell, RFK Jr.'s latest antivax stunt runs counter to the WMA Declaration of Helsinki. Withholding HepB vaccination clearly does not meet any definition of clinical equipoise. Doing it anyway, overseas, is straight up colonialist medicine. Details in Dr. Jacobs's thread below.
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
nature.com
Registration is now open for @keystonesymposia.bsky.social "Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection." Deadline for scholarships and abstract selected short talks is Jan 7! Join us this May for an amazing meeting! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26
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
Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host. Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social) Registrants will receive free memberships to Applied Microbiology International. Details below 👇
ISB@isbscience.org · 9mo agoJoin @isbscience.org on December 12 for a Virtual Microbiome Symposium highlighting new discoveries about how gut-derived metabolites affect neural, immune, and endocrine systems. Open to microbiome-curious researchers and practitioners everywhere. isbscience.org/events/2025-...
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
#NewResearch Strain displacement in microbiomes via ecological competition @erikbakkeren.bsky.social #microsky 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
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 · 2y 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!)
Preprint alert! I’m excited to share my work identifying and characterizing the impact of fungal-bacterial nutrient sharing in the vaginal tract 🦠
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 11mo agoA fungal pathobiont promotes Streptococcus agalactiae vaginal persistence and pathogenesis through physical and metabolic interactions https://www.biorxiv.org/content/10.1101/2025.09.07.674778v1
Thrilled to share @alex-dobrila.bsky.social’s new review in Infection & Immunity on how butyrate shapes C. difficile pathogenesis. A must-read for those interested in microbiome–pathogen interactions. 👉 journals.asm.org/doi/10.1128/...
The emerging view on the roles of butyrate in Clostridioides difficile pathogenesis | Infection and Immunity
The Centers for Disease Control and Prevention classifies Clostridioides difficile as an urgent threat to the nation’s health, as it causes 450,000 infections, 15,000 deaths, and 1 billion dollars in excess healthcare costs per year in the United States (1, 2). Most C. difficile infections (CDIs) occur in healthcare settings, where CDI is the most common cause of infectious diarrhea (3). Known and suspected risk factors for CDI include antibiotics, proton pump inhibitors, impaired immune function, advanced age, and diet, all of which are associated with dysbiotic gastrointestinal (GI) microbiomes (4–6). Though most CDIs are associated with antibiotic treatment, 22% of individuals with community-acquired CDI have no recent history of antibiotic use. Factors affecting persistent and recurrent CDIs remain poorly defined (7, 8). Despite the morbidity and mortality caused by C. difficile, up to 15% of healthy adults are asymptomatic carriers of toxigenic C. difficile (9), highlighting the gaps in our understanding of C. difficile.
journals.asm.org
Happy to see this out and congrats to lead author Anaïs! Sulfide is an under explored metabolite in the gut due to its volatility making quantification very difficult, so it's exciting to see new research out exploring its effects on the microbiota!
Andreas Bäumler@abaumler.bsky.social · 11mo agoHydrogen sulfide production distinguishes Salmonella from close relatives, but its biological significance remains obscure. This study uncovers the secret: Salmonella uses hydrogen sulfide production as a weapon to outcompete E. coli and gain a foothold in the gut. www.pnas.org/doi/10.1073/...
Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.
Commensal yeast promotes Salmonella Typhimurium virulence - Nature
Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.
nature.com
Happy to see the preview @joeyzacks.bsky.social and I wrote on the excellent paper recently published by the Gibbons Lab @gibbological.bsky.social is in press! I'd encourage folks interested in bacterial pathogenesis or microbial ecology to check out the preview and the research article!
Microbial bellwether: Community-scale metabolic modeling to predict infection
Microbial colonization is shaped by a complex network of interactions that influence both commensals and pathogens, including the public-health threat…
sciencedirect.com
1/ Excited to share the first preprint from my lab! 🎉 My postdoc Paz asked how cholera toxin (CT) helps Vibrio cholerae thrive in the gut. Turns out, CT rewires epithelial metabolism toward L-lactate production—fueling pathogen growth in the small intestine during disease
Cholera toxin-induced disease generates epithelial cell-derived L-lactate that promotes Vibrio cholerae growth in the small intestine
Cholera toxin (CT) promotes Vibrio cholerae colonization by altering gut metabolism to favor pathogen growth. We have previously found that CT-induced disease leads to increased concentrations of L-la...
biorxiv.org
I’m excited to share my recent study from the labs of @joeyzacks.bsky.social and @ritatamayo.bsky.social on the impact of E.faecalis on phase variable behaviors in C.difficile. This work was achieved through amazing co-leadership with PhD candidate Jilarie Santos-Santiago.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.Enterococcus faecalis modulates phase variation in Clostridioides difficile https://www.biorxiv.org/content/10.1101/2025.07.24.666506v1
💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥 I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com @cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social www.cell.com/cell-systems... 🧵...
Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut
Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...
cell.com
