Connor Tiffany

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...

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...

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 ...

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...

Very cool study and impressive work! Congrats! @qianxuan.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...

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

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.

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-...

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.

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 ...

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...

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!

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

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 👇

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

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.

#NewResearch

Strain displacement in microbiomes via ecological competition

@erikbakkeren.bsky.social

#microsky

www.nature.com/articles/s41...

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!

Preprint alert! I’m excited to share my work identifying and characterizing the impact of fungal-bacterial nutrient sharing in the vaginal tract 🦠

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.

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/...

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!

Commensal yeast promotes Salmonella Typhimurium virulence - Nature Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

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.

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...

And here is a link to the Gibbons Lab paper!

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…

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!

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...

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

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.

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...

💥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...

🧵...

This is fantastic work and I'm excited to see it in press! Congrats to all involved!

Happy to see that this fantastic work is in press now! Congrats to the Palmer lab and lead authors @xiaomeiren.bsky.social and @rmasonclark.bsky.social.

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.

Excited to share this collaborative study with @ritatamayo.bsky.social showing that E. faecalis influences C. diff morphology through the phase variable CmrRST system! This work was co-led by the amazing team of @ashleyweiss.bsky.social and Jilarie Santos-Santiago!

This is anectodal, but for my own coding the only things that AI can do correctly I can do quicker than it takes to write a prompt that generates something useful. I figured productivity gains were over hyped but yikes lol

Philly will stop functioning if these cuts happen, and if Philly doesn't function, Pennsylvania's economy will crash and burn.