MICROBIOMES FACULTY OPPORTUNITY

The USF Institute of Microbiomes is recruiting four well-funded researchers to expand its growing research portfolio and strengthen USF Health’s national leadership in microbiome science, translational medicine, and precision health. The new investigators will advance multidisciplinary research in areas including host-microbiome interactions, infectious diseases, immunology, cancer, metabolic disorders, and other emerging fields of biomedical science.

FEATURED ARTICLES

Emerging USF Research Spotlight: 

USF cancer research gets shot in the arm with $6 million in state awards

Researchers at the University of South Florida and Tampa General Hospital Cancer Institute are advancing microbiome-focused cancer research through two state-funded projects led by Rays H. Y. Jiang, PhD. In one project, Timothy Yeatman, MD, PhD, serves as principal investigator with Dr. Jiang as co-investigator to map the tumor microenvironment by analyzing microbes, lipids, and gene activity at the single-cell level to identify new therapeutic targets. A second project, led by Richard Jacobson, MD, with Dr. Yeatman and Dr. Jiang as co-investigators, will examine how dietary fats influence gut bacteria, their metabolites, and tumor signaling to determine whether these interactions can make the liver less favorable for colorectal cancer metastasis. Together, these studies highlight the growing role of the microbiome in precision cancer medicine and the development of more personalized treatment strategies.

Two New Studies Advance Understanding of

Microbiome-Gut-Brain Signaling

New Publications

Microbiome Maturation May Help Predict Type 1 Diabetes Risk

A study published September 21 in Nature Metabolism examined how gut microbiome development during early childhood interacts with genetic susceptibility to type 1 diabetes. Researchers found that differences in microbiome maturation were associated with future disease risk, suggesting that tracking the developing gut microbiome could potentially help identify children at especially high risk and provide new insight into the early biological processes involved in type 1 diabetes. (Nature)

Gut Microbiome Signals May Predict Necrotizing Enterocolitis in Premature Infants

Researchers at Washington University School of Medicine identified gut microbial features that may predict necrotizing enterocolitis (NEC), a serious intestinal disease affecting premature infants, before symptoms develop. Analyzing stool samples, researchers found that bacteriophages—viruses that infect bacteria—and bacterial antibiotic-resistance genes could distinguish infants who later developed NEC. Predictive models identified early-onset disease up to eight days before symptoms with approximately 75% accuracy and late-onset disease with 83% accuracy, raising the possibility of earlier intervention for vulnerable infants. (The Source)

Gut Microbiota May Be a Strong Indicator of Systemic Inflammation

A Nature Communications study of 1,199 adults found that gut microbiota composition explained more variation in many inflammatory and physiological measures than chronological age. Researchers identified a Bacteroides 2 enterotype associated with elevated inflammatory markers and adverse metabolic characteristics appearing decades earlier than in other microbiome profiles. The findings suggest that microbial composition may offer additional insight into differences in inflammatory aging and future disease risk. (Nature)

Fecal Microbiota Transplantation Explored as a Strategy for Crohn’s Disease

An open-label pilot study investigated whether fecal microbiota transplantation (FMT) could reduce mucosal colonization by adherent-invasive Escherichia coli (AIEC), a bacterium implicated in Crohn’s disease. Thirty adults received a single colonoscopic FMT, and researchers observed AIEC decolonization in all eight evaluable participants who were positive for the bacterium at baseline. No FMT-related serious adverse events were reported. The preliminary findings support further investigation of microbiome-based approaches targeting specific microbial populations in Crohn’s disease. (Nature)

Microbiome Transplants Show Potential for Treating Peanut Allergy

An NIH-funded early-stage clinical trial tested whether oral fecal microbiota transplantation could increase tolerance to peanuts in people with peanut allergy. Fifteen participants received capsules containing microbes from donors without food allergies. Four months later, six participants—including three who received antibiotics before transplantation and three who did not—were able to tolerate increased amounts of peanut. The response was associated with changes in immune T cells, providing additional evidence that manipulating the gut microbiome could eventually contribute to new approaches for food-allergy treatment. (National Institutes of Health)

Antifungal Therapy Reshapes the Gut Microbiome in IBD

A prospective study published in Nature Medicine compared two antifungal treatments in 53 patients with mild-to-moderate inflammatory bowel disease and oral thrush. Fluconazole, which acts throughout the gastrointestinal tract, reduced intestinal Candida, increased bacterial diversity and short-chain-fatty-acid-producing bacteria, and altered microbial metabolites and cross-kingdom microbial networks. These microbiome changes coincided with improved measures of disease activity, although the observational study was not designed to establish treatment efficacy. The findings highlight the potential of targeting the gut mycobiome as part of precision approaches to IBD. (Nature)

Gut Microbial Metabolite Linked to Primary Sclerosing Cholangitis

Researchers have identified the gut microbiota-derived metabolite imidazole propionate (ImP) as a potential contributor to primary sclerosing cholangitis (PSC), a chronic inflammatory disease of the bile ducts. Patients with PSC had higher circulating ImP concentrations, and higher levels were associated with reduced survival. Experiments also showed that prolonged ImP exposure promoted liver inflammation and fibrosis through p38 signaling. The findings provide new mechanistic insight into the gut–liver axis and suggest that microbial metabolite production or signaling could become a target for future therapies. (LTNR)

Microplastics May Promote Antibiotic Resistance in Soil Microbiomes

Several recent studies are highlighting interactions between microplastics, environmental microbiomes and antibiotic resistance. One study found that opportunistic microbial taxa contributed to the proliferation of antibiotic-resistance genes in soils contaminated with both microplastics and tetracycline. Other September research showed that microplastic aging can alter the microbial communities and resistance genes associated with the “plastisphere,” while microplastics can also influence movement of resistance genes through soil–plant systems. Together, the findings underscore the potential role of environmental microbiomes in the spread of antimicrobial resistance. (Nature) 

Sugar-Rich Diets May Intensify Antibiotic-Related Gut Microbiome Disruption

A Nature study examining patients undergoing hematopoietic cell transplantation found that higher consumption of sweets and simple sugars during broad-spectrum antibiotic treatment was associated with greater loss of gut microbial diversity and increased expansion of Enterococcus. Mouse experiments produced similar findings, suggesting that sucrose may intensify and prolong antibiotic-associated microbial disruption. The researchers note that diet could potentially become a modifiable factor for protecting the gut microbiome during antibiotic therapy, although clinical trials are needed to confirm the effect.

Read the article in Nature

Distinct Gut Microbiome Patterns Identified Across Cancer Types

Mayo Clinic researchers analyzed stool samples from 1,364 patients and identified distinct gut microbiome patterns associated with five cancer groups, as well as differences between early- and later-onset cancers. In early-onset colorectal cancer, researchers found higher lactate levels and increased abundance of Veillonella parvula. Microbial features were also linked with cancer survival and chemotherapy toxicity, highlighting the potential future role of microbiome profiling in precision oncology.

Read the Mayo Clinic article

Early-Life C. difficile Exposure May Produce Lasting Changes in the Gut

NIH-supported research suggests that exposure to Clostridioides difficile during early life may have long-term effects on intestinal development. In newborn mice, early exposure altered intestinal stem cells, mucus-producing cells and immune-related functions in ways that persisted into adulthood. Although infants colonized with C. difficile often do not develop the severe illness seen in adults, the findings add to evidence that microbial exposures during critical periods of development may have lasting consequences for gut biology and immune function.

Read the NIH Research Matters article

Coffee Consumption Linked to the Gut Microbiome and Gut–Brain Axis

Research published in Nature Communications examined how habitual coffee consumption influences the microbiota–gut–brain axis. Coffee drinkers showed differences in gut microbial composition and metabolites, while behavioral and cognitive measures also varied between coffee-drinking and non-coffee-drinking groups. Some metabolomic changes reversed during coffee abstinence and reappeared after coffee was reintroduced, supporting further investigation into interactions among coffee compounds, gut microbes and brain-related functions.

Read the study in Nature Communications

Gut Microbiome Patterns May Help Identify Type 2 Diabetes Risk Earlier

Research presented at the European Association for the Study of Diabetes annual meeting analyzed microbiome and health data from 229,025 adults in the United Kingdom and United States. Researchers identified 789 bacterial species associated with type 2 diabetes and found that diabetes-associated microbial patterns were also detectable in people with prediabetes and some individuals with normal conventional blood glucose measurements but signs of insulin resistance. The researchers emphasize that microbiome analysis would complement rather than replace existing diabetes testing.

Read the Medical Xpress article

Periodontal Disease May Influence Bone Loss Through the Gut Microbiome

Research from Griffith University and Nanjing University suggests that periodontal disease may contribute to osteoporosis through alterations in the gut microbiome and systemic inflammation. The researchers propose an oral–gut–bone axis that could help explain the previously observed association between periodontitis and bone loss. The findings highlight another example of how microbial disturbances originating at one body site may influence health elsewhere in the body.

Read the article on Technology Networks

2025-2026 USF Microbiome Research Awards

We are accepting applications for the Ignite Award.

These awards are intended to be small, rapid-access awards to 1) help investigative teams maintain momentum on feasibility projects with a high probability of traversing research gaps related to microbiome research, 2) obtain pilot data that will allow for the submission of a subsequent, more extensive extramural grant application, or 3) provide internal funding for new research projects that have been peer-reviewed and scored to help move grants to a fundable range.

Funds will be awarded for up to $5,000 to be spent within a maximum of 3 months of the award. This application process will be rolling, with investigators invited to apply at any time that is convenient to them.

The University of South Florida Initiative on Microbiomes is partnering with the Global Virus Network to offer the online course Microbiomes and their Impact on Viral Infections.

Taught by world-renowned expert instructors, this self-paced, certified, non-credit course will provide you with the latest knowledge on the importance and role of the microbiome in preventing, mitigating, and treating diseases.

FOUNDATION & PROFESSIONAL ASSOCIATION GRANTS

Diet-Microbiome Interactions Shaping Immune Function in the Treatment of Human Disease

Sponsor: Biocodex Microbiota Foundation

Due Date:  November 30, 2026

For more information, click HERE.

AGA Research Scholar Award (RSA)

Sponsor: American Gastroenterological Association Research Foundation

Funding: $300,000 over three years ($100,000 per year).

Eligibility: Early-career faculty working toward an independent research career in digestive disease; applicants must meet AGA eligibility requirements.

Relevance to microbiomes: Potential fit for gut microbiome, host–microbe interaction, microbial metabolite, nutrition, and other microbiome studies that are directly relevant to digestive diseases.

Application due date: December 2, 2026

Full funding announcement HERE.

AGA-Takeda Pharmaceuticals Research Scholar Award in Inflammatory Bowel Disease

Sponsor: American Gastroenterological Association Research Foundation / Takeda Pharmaceuticals

Funding: $300,000 over three years ($100,000 per year).

Eligibility: Early-career faculty pursuing an independent research career in inflammatory bowel disease (IBD).

Relevance to microbiomes: Strong potential fit for IBD-focused studies of gut microbiome composition and function, host–microbe interactions, microbial metabolites, mucosal immunity, or microbiome-targeted interventions.

Application due date: December 2, 2026

Full funding announcement HERE.

Clinical Research Award

Sponsor: American College of Gastroenterology

Application due date: December 7, 2026

Relevance to microbiomes: This grant is designed to support research that is principally focused on digestive or liver diseases. The patient population or disease target should be principally related to the gastrointestinal tract, liver, biliary system, pancreas, or neuroenteric science, including any translational, clinical, social science, or health services research studies that pertain to managing such patients or conditions. For example, a study about microbiota would be appropriate if it pertains to a digestive disease.

Full funding announcement HERE.

Microbiota & Women's Health International Call for Projects

Sponsor: Biocodex Microbiota Foundation

Due Date: January 15, 2027

For more information, click HERE.

NSF

Core Research in Biological Sciences (BIO Core)

Sponsor: U.S. National Science Foundation (NSF)

Program Solicitation: NSF 26-517

Funding: NSF anticipates approximately $280 million across 250–300 awards; individual budgets and durations vary by project scope.

Relevance to microbiomes: Supports foundational and interdisciplinary biology from molecular to biome scales. Microbiology, genomics, quantitative biology, microbial ecology, community interactions, environmental microbiomes, and development of biological tools and datasets can fit within the program.

Application deadline: Proposals accepted anytime.

Full funding announcement HERE.

USDA-NIFA

Agricultural Microbiomes in Plant Systems and Natural Resources (A1402)

Sponsor: USDA National Institute of Food and Agriculture (NIFA), Agriculture and Food Research Initiative (AFRI)

Status: FY2027 NOFO and application deadlines are forthcoming.

Relevance to microbiomes: A recurring AFRI program area priority focused on agricultural microbiomes in plant systems and natural resources. It is particularly relevant to plant, soil, environmental, agricultural, and One Health microbiome research.

Program and deadline information HERE.

AFRI Food Safety, Nutrition, and Health Program Area

Sponsor: USDA National Institute of Food and Agriculture (NIFA)

Status: FY2027 Foundational and Applied Science NOFO deadlines are forthcoming.

Relevance to microbiomes: Potential fit for food and human health, diet and chronic disease, food safety, antimicrobial resistance, and nutrition studies in which the microbiome is a central mechanism or outcome. The program area also encompasses Agricultural Microbiomes in Plant Systems and Natural Resources.

Program information HERE.

NIH

Resource-Related Research Projects for Development of Models and Related Materials for Studying Human Health and Diseases (R24 Clinical Trials Not Allowed)

Sponsor: NIH

Funding Opportunity Number: PAR-25-416

Application due dates: January 26, 2027

Relevance to microbiomes: Development of information resources for generating novel hypotheses and improving the utilization of animals in biomedical research, including deep phenotyping of organelles, single cells, cellular networks, microbiomes, or behaviors.

Full funding announcement HERE.

Enhancing Mechanistic Research on Precision Probiotic Therapies — R61/R33

Sponsor: NIH

Funding Opportunity Number: PAR-25-211

Relevance to microbiomes: This phased program supports research into why people respond differently to probiotic interventions. Relevant variables can include baseline microbiome composition, immunity, diet, age, genetics, lifestyle, and health history. The R61 phase identifies patterns associated with probiotic responses; successful projects can move into an R33 mechanistic validation phase.

Application due date: June 2, 2027

Full funding announcement HERE.

Enhancing Mechanistic Research on Precision Probiotic Therapies — R33

Sponsor: National Institutes of Health

Opportunity number: PAR-25-210

Relevance to microbiomes: Supports later-stage mechanistic studies in which investigators already have preliminary evidence of host or microbiome characteristics associated with probiotic response. Projects should test the causality or predictive value of these characteristics using human studies or rigorous experimental models.

Application Due Date: June 2, 2027

Full funding announcement HERE.

Basic Research in Cancer Health Disparities (R01 Clinical Trial Not Allowed)

Sponsor: NIH, National Cancer Institute (NCI)

Relevance to microbiomes: Role of the microbiota in cancer disparities during tumorigenesis, progression, and response to therapy.

Application due date: February 05, 2027

Full funding announcement HERE.

Advancing Bioinformatics, Translational Bioinformatics and Computational Biology Research — R01

Sponsor: NIH/National Institute of General Medical Sciences

Funding Opportunity Number: PAR-26-040

Relevance to microbiomes: The announcement specifically identifies microbiome studies, host–microbiome interactions, metagenomics, and metaproteomics as areas of interest. It prioritizes broadly applicable computational methods, pipelines, and resources over narrowly focused analyses of a single dataset.

Next application due dates: October 5, 2026, February 05, 2027

Full funding announcement HERE.

NIH Parent R01 — Clinical Trial Not Allowed

Sponsors: Multiple NIH institutes

Funding Opportunity Number: PA-25-301

Relevance to microbiomes: NIH has designated multidisciplinary mechanistic microbiome science as a highlighted research topic through January 15, 2028. Investigators may submit relevant work through this Parent R01 when the project fits the mission of a participating institute.

Areas encouraged by NIH include host–microbiome molecular interactions, microbial metabolites, microbiome-informed diagnostics, disease prevention, cancer treatment response, infectious disease, immune-mediated disease and microbiome-targeted interventions.

Application due date: February 5, 2027

Full funding announcement: NIH Parent R01

Mechanisms that Impact Cancer Risk after Bariatric Surgery (R21 Clinical Trial Not Allowed)

Sponsors: NIH, National Cancer Institute

Next due dates: October 16, 2026, February 16, 2027

Relevance to microbiomes: How do changes in the GI microbiome after BS affect metabolite pools and interactions with host (epithelial and immune) tissues?

Funding Opportunity Number: PAR-25-044

Full funding announcement HERE.

NIH Parent R21 — Clinical Trial Not Allowed

Sponsor: Multiple NIH institutes

Funding Opportunity Number: PA-25-304

Relevance to microbiomes: The R21 supports exploratory and developmental projects that may carry higher risk but could produce new concepts, tools, models, agents or methodologies. It is particularly relevant for microbiome pilot studies that are not yet ready for a full R01.

Application due dates: October 16, 2026, February 16, 2027

Full funding announcement: NIH Parent R21

Advancing Nutrition Research to Inform Regulatory Practice — NIH Highlighted Topic

Sponsor: National Institutes of Health (multiple participating institutes and offices)

Status: Highlighted topic active through March 20, 2028; this is not a standalone NOFO. Applications are submitted through an appropriate NIH Parent Funding Announcement or other broad NIH opportunity.

Relevance to microbiomes: Potential fit for mechanistic nutrition research involving dietary patterns, food components, ultra-processed foods, metabolic health, biomarkers, and microbiome-related pathways when aligned with the objectives of a participating NIH institute or center.

Highlighted topic information HERE.

Breaking Barriers: Integrating Immunology and Neuroscience to Transform AD/ADRD Research and Bring a Better Understanding of the Aging Brain — NIH Highlighted Topic

Sponsor: National Institutes of Health; participating institutes include NIA and NIAID

Status: Highlighted topic active through May 1, 2028; this is not a standalone NOFO. Applications are submitted through an appropriate NIH Parent Funding Announcement or other broad NIH opportunity.

Relevance to microbiomes: Particularly relevant to gut–immune–brain and neurodegeneration research. NIAID specifically identifies immune mechanisms connecting infectious exposures to neurodegeneration, including the role of the microbiome and its metabolites.

Highlighted topic information HERE.

Food Is Medicine — NIH Highlighted Topic

Sponsor: National Institutes of Health (multiple participating institutes and centers)

Status: Highlighted topic active through June 3, 2028; this is not a standalone NOFO. Applications are submitted through an appropriate NIH Parent Funding Announcement or other broad NIH opportunity.

Relevance to microbiomes: Potential fit for multidisciplinary studies examining how diet, food-based interventions, and microbiome-mediated mechanisms influence obesity, diabetes, cardiovascular disease, cancer, mental health, or other diet-related chronic diseases.

Highlighted topic information HERE.