UCSF Benioff Center for Microbiome Medicine
 

August 2026

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Feature News

Building Connections: Highlights from the BCMM Retreat



Our annual BCMM Retreat at the Chaminade Resort and Spa in Santa Cruz, CA, was a resounding success, bringing together 70 participants for an inspiring and productive event. The retreat provided a unique opportunity to exchange cutting-edge research, foster collaborations, and enjoy a variety of community-building activities. The program featured a keynote lecture by Dr. Suzanne Devkota, whose work focuses on the interplay between the gut microbiome, diet, and human health. The retreat also included guest lectures by BCMM alumni Drs. Joel Babdor and Margaret Alexander, who presented their current work but also led a discussion with trainees on the transition from postdoc to faculty positions. They shared invaluable advice on navigating the early stages of launching a new lab, including the dos and don’ts critical to success.


In addition to the scientific sessions, retreat attendees had the chance to participate in organized pickleball and dodgeball tournaments during the afternoon, fostering camaraderie and teamwork. The evening reception offered a relaxed atmosphere for networking and discussions, while the poster session showcased the cutting-edge research being conducted within our community. The BCMM congratulates the winners of the poster competition:


Taylor Halsey (Turnbaugh lab) - 1st place (postdoc)

Rafaella Shima (Turnbaugh lab) - 1st place (grad student)

Lea Twicken (Nayak lab) - 1st place (staff)


Rebecca Knoll (Lynch lab) - 2nd place (postdoc)

Mikaela Matera-Vatnick (Turnbaugh lab) - 2nd place (grad student)

Punit Sundaramurthy (Lynch lab) - 2nd place (staff)



Reflecting on the retreat’s tremendous success, we are thrilled to announce that planning for our next retreat is already underway. Stay tuned for updates on what’s to come.

Leisure time

Poster competition

Poster winners

News

BCMM welcomes 12 summer undergraduate interns


This summer, BCMM labs are hosting 12 talented undergraduate interns, each bringing enthusiasm, creativity, and curiosity to the field of microbiome research. Over the summer, these students will immerse themselves in a variety of impactful research projects, gaining hands-on experience and working alongside BCMM faculty, researchers, and staff to advance our understanding of microbial communities and their roles in human health.


The interns will contribute to research initiatives across several BCMM labs and facilities, including the Ott Lab, Lynch Lab, Johnson Lab, Turnbaugh Lab, Upadhyay Lab, Scharschmidt Lab, Torgerson Lab, and Roan Lab, as well as the BCMM Genomics & Microbial Culturing Facility. Under the mentorship of lab personnel, the interns will acquire valuable technical skills, engage in data analysis, and participate in discussions designed to foster their growth and development.


At BCMM, we are committed to nurturing the next generation of scientists, innovators, and leaders in microbiome medicine. Hosting summer interns gives junior researchers the opportunity to contribute to cutting-edge research while exploring career paths in science and medicine. By collaborating with BCMM’s researchers, these students will gain firsthand experience in a dynamic and collaborative scientific environment.

Tiffany Scharschmidt, MD

Katrina Abuabara, MD

Celebrating BCMM excellence: Katrina Abuabara and Tiffany Scharschmidt receive 2026 ARCHES awards


We are incredibly proud to share that two of our very own BCMM members, Katrina Abuabara, MD and Tiffany Scharschmidt, MD, are among this year's cohort of ten outstanding UCSF faculty members who were recently selected as recipients of the prestigious 2026 ARCHES Mid-Career Development Awards.


The ARCHES program is a robust, two-year initiative designed for research faculty who aren't just exceptional scientists, but also outstanding mentors. It specifically recognizes individuals who have demonstrated a deep commitment to UCSF's PRIDE Values and Principles of Community. By providing protected time, dedicated mentorship, and a collaborative network, the program invests in faculty at pivotal stages of their careers to help them expand their leadership and accelerate their research. Both Katrina and Tiffany, representing the School of Medicine's Department of Dermatology, embody exactly what this award stands for. Their dedication to pushing the boundaries of biomedical discovery while actively uplifting the next generation of researchers makes this recognition incredibly well-deserved.

 

BCMM publishes annual impact report


The Benioff Center for Microbiome Medicine (BCMM) is proud to share its 2026 impact report, showcasing key achievements and growth in microbiome science over the past year. Highlights include:

  • Groundbreaking Biotherapeutics: Research originating from the Lynch Lab led to STMC-103H, a live biotherapeutic that reduces the risk of atopic dermatitis by 64% and food allergies by 77% in high-risk infants, revolutionizing disease prevention.
  • Expanded Infrastructure: BCMM invested in state-of-the-art facilities like the new Quantitative Metabolite Analysis Center (QMAC) and cutting-edge tools like the Thermo Orbitrap Exploris 240 GCMS, advancing metabolomics and microbiome research capacity.
  • Growing Community: BCMM welcomed 41 new members, bringing total membership to over 200 researchers, and produced 54 microbiome-related publications, reflecting strong interdisciplinary collaboration.
  • Training Future Leaders: New programs, including grant-writing workshops, technology access initiatives, and hands-on sequencing training, empower researchers to lead impactful microbiome studies.



BCMM’s progress underscores its commitment to transforming microbiome science into medicine. Thank you to our donors for your continued support in advancing this vital work!

Publications

Steininger HM, McCauley KE, Braga GE, Morin A, Lee KE, Visness CM, Fadrosh DW, Dapas M, O'Connor GT, Bacharier LB, Rivera-Spoljaric K, Kattan M, Lemanske RF Jr, Zoratti EM, Martinez FD, Gold DR, Hartert TV, Johnson CC, Miller RL, Seroogy CM, Wood RA, Togias A, Jackson DJ, Gern JE, Ober C, Lynch SV; CADRE investigators. Upper Airway Microbiome Interacts with GSDMB and ORMDL3 Asthma Risk SNPs to Influence Early-Life Wheeze Risk. J Allergy Clin Immunol. 2026 Jun 4:S0091-6749(26)00405-7. doi: 10.1016/j.jaci.2026.05.021. Epub ahead of print. PMID: 42248217.

Babdor J, Patel RK, Davidson B, Koser K, Noecker C, Rahim MK, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy EE, Shaheed A, Ekstrand C, Weakley AM, Yu FB, Krip K, Shaikh KA, Amatullah H, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH. Immune-microbiome coordination defines interferon setpoints in healthy humans. Cell. 2026 May 14;189(10):3144-3163.e20. doi: 10.1016/j.cell.2026.02.003. Epub 2026 Mar 9. PMID: 41806833; PMCID: PMC13137166.

Herzog HM, Fang C, Lam L, Jin K, Zamarioli A, Dinh E, Gupta CL, Sharma A, Moody T, Pierce JL, Hohl MS, Takimoto SW, Lyalina S, Wentworth KL, Yu K, Lu VF, Mamikunian I, Hunt NK, Lynch S, Pollard KS, Hernandez CJ, Perrien DS, Hsiao EC. Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1R206H-driven heterotopic ossification. bioRxiv [Preprint]. 2026 Apr 8:2026.04.05.716562. doi: 10.64898/2026.04.05.716562. PMID: 41993555; PMCID: PMC13081864.

Touhara KK, Xu J, Castro J, Liang HE, Li G, Brizuela M, Harrington AM, Garcia-Caraballo S, O'Donnell T, Neumann D, Rossen ND, Deng F, Schober G, Li Y, Locksley RM, Brierley SM, Julius D. Parasites trigger epithelial cell crosstalk to drive gut-brain signalling. Nature. 2026 May;653(8114):465-473. doi: 10.1038/s41586-026-10281-5. Epub 2026 Mar 25. PMID: 41882357; PMCID: PMC13171452.

Dubinkina V, Smith BJ, Zhao C, Pino C, Pollard KS. Linkage of nucleotide and functional diversity varies across gut bacteria. Proc Natl Acad Sci U S A. 2026 May 12;123(19):e2521012123. doi: 10.1073/pnas.2521012123. Epub 2026 May 6. PMID: 42090264; PMCID: PMC13168539.

Santarossa S, Sitarik AR, Houck FL, Brawner CA, Johnson CC, Comstock SS, Lynch SV, van Wyk PM, Vundla F, Schachtschneider C, Straughen JK, Cassidy-Bushrow AE. Association between objectively measured physical activity and maternal stool microbiota during pregnancy: results from a preliminary investigation. Front Cell Infect Microbiol. 2026 Apr 23;16:1747305. doi: 10.3389/fcimb.2026.1747305. PMID: 42112457; PMCID: PMC13149394.

Zhang S, Buttimer C, Trepka KR, Lam KN, Ramirez Hernandez LA, Soto-Perez P, Noecker C, Canigiula P, Ortega EF, Lee J, Ramirez L, Partipilo G, Lawrence HB 3rd, Bottacini F, Draper LA, Paul Ross R, Coffey A, Shkoporov A, Hill C, Turnbaugh PJ. Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters. Res Sq [Preprint]. 2026 May 5:rs.3.rs-9488777. doi: 10.21203/rs.3.rs-9488777/v1. PMID: 42147160; PMCID: PMC13174815.

Tsai W, Zhu F, Bar-Or A, Bernstein CN, Bonner C, Graham M, Marrie RA, Mirza AI, O'Mahony J, Yeh EA, Banwell B, Waubant E, Tremlett H; Canadian Pediatric Demyelinating Disease Network. The gut microbiome in pediatric-onset acquired demyelinating syndromes by myelin oligodendrocyte glycoprotein antibody status. Mult Scler Relat Disord. 2026 Jun;110:107216. doi: 10.1016/j.msard.2026.107216. Epub 2026 Apr 27. PMID: 42068931.

Lydon EC, Deosthale P, Glascock A, Phan HV, Osborne CM, Leroue MK, Allen J, Mick E, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway. Nat Commun. 2026 Apr 13;17(1):5149. doi: 10.1038/s41467-026-71863-5. PMID: 41974724; PMCID: PMC13250161.

Bodkhe RL, Blank RB, Trepka KR, Orellana DA, Scher JU, Turnbaugh PJ, Nayak RR. Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis. bioRxiv [Preprint]. 2026 Mar 30:2026.03.30.715090. doi: 10.64898/2026.03.30.715090. PMID: 41959277; PMCID: PMC13060180.

Wang S, Guitor AK, Valentin-Alvarado LE, Garner R, Zhang P, Yan M, Shi LD, Schoelmerich MC, Steininger HM, Portik DM, Zhang S, Wilkinson JE, Lynch S, Morowitz MJ, Hess M, Diamond S, Banfield JF, Sachdeva R. Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains. bioRxiv [Preprint]. 2026 Mar 28:2026.03.27.714056. doi: 10.64898/2026.03.27.714056. PMID: 41929113; PMCID: PMC13041992.

Noecker C, Guo L, Daté C, Rai N, Daramy F, Ramirez Hernandez LA, Kyaw TS, Trepka KR, Gupta CL, Ha CWY, Babdor J, Spitzer MH, Turnbaugh PJ. A widespread gut bacterial lineage distinguished by redox metabolism and phage defense. bioRxiv [Preprint]. 2026 Apr 1:2026.03.31.715625. doi: 10.64898/2026.03.31.715625. PMID: 41959463; PMCID: PMC13060105.

Rock RR, Alexander M, Noecker C, Trepka KR, Upadhyay V, Ortega EF, Ramirez L, Siewert L, Olson CA, Halsey T, Pröbstel AK, Baranzini SE, Turnbaugh PJ. Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2. bioRxiv [Preprint]. 2026 Mar 23:2026.03.16.711194. doi: 10.64898/2026.03.16.711194. PMID: 41928970; PMCID: PMC13042044.

Bloom SM, Symul L, Elsherbini J, Xu J, Hussain S, Shih J, Sango A, Mitchell CM, Hemmerling A, Parks TP, Kannan A, Hussain FA, Cohen CR, Holmes SP, Kwon DS. Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial. Cell Host Microbe. 2026 Apr 8;34(4):734-750.e10. doi: 10.1016/j.chom.2026.03.003. Epub 2026 Mar 27. PMID: 41903526.

Hotca AE, Lin OM, Piawah S, Mendiola DM, Yom SS, Kuon C, Atreya CE. The Role of the Microbiome and Gut Health in Patients With Digestive Tract Cancers. Semin Radiat Oncol. 2026 Jul;38:151032. doi: 10.1016/j.semradonc.2026.151032. PMID: 42288363.

Dubin CA, Zhao C, Pollard KS, Oskotsky T, Golob JL, Sirota M. Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia. mSystems. 2026 Jun 23;11(6):e0149825. doi: 10.1128/msystems.01498-25. Epub 2026 Jun 3. PMID: 42233644; PMCID: PMC13289165.

Correale J, Marrodan M, Piedrabuena MA, Soman K, Farez MF, Baranzini SE. Microbiome-derived metabolites from vitamin B2 and B9 pathways modulate MAIT cells from multiple sclerosis patients. Mult Scler. 2026 Jun 1:13524585261447695. doi: 10.1177/13524585261447695. Epub ahead of print. PMID: 42224283.

Lieberman OJ, Nittala S, Rojas-Valencia L, Baranzini SE, Singhal NS, Hemphill JC, Amorim E, Ferguson AR, Hinson HE. Circulating Short-Chain Fatty Acid Profile Predicts Functional Outcome After Moderate-to-Severe Traumatic Brain Injury. Crit Care Explor. 2026 Jun 11;8(6):e1433. doi: 10.1097/CCE.0000000000001433. PMID: 42268644; PMCID: PMC13259564.

Golan Y, Nyquist SK, Liu Z, Ennis D, Zhao J, Blair E, Khan AR, Prahl M, Gaw SL, Yassour M, Engelhardt BE, Flaherman VJ, Ahituv N. Genomic characterization of normal and aberrant human milk production. Sci Adv. 2025 Sep 12;11(37):eadr7174. doi: 10.1126/sciadv.adr7174. Epub 2025 Sep 10. PMID: 40929253; PMCID: PMC12422191.

 
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