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Microbiomes Institute

Microbiomes Institute

2023-2024 Microbiome Research Awards

We are currently 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 high probability of traversing research gaps related to microbiome research, 2) obtain pilot data that will allow for the submission of a subsequent, larger 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.   

Please click the below links for the full details and application instructions:


2022-2023 Microbiome Research Award winners:

Pilot awards

Therapeutic potential of a unique postbiotic using a TDP-43 mouse model
PI: Umesh Jinwal, PhD
Associate Professor, Department of Pharmaceutical Sciences, USF College of Pharmacy  

Investigating the impact of long-term systemic NMDA antagonist in retina: Role of gut microbiome & metabolites
PI: Manas R. Biswal, M.F.Sc., Ph.D.
Assistant Professor, Department of Pharmaceutical Sciences and Graduate Programs, College of Pharmacy

Ignite Awards

Association of Microbiome with Dysregulated Inflammation and Cardiometabolic Disease: An Ancillary Study of the Microbiome in Aging Gut and Brain (MiaGB) Study
PI: Nicholas W. Carris, PharmD
Associate Professor, TCOP Dept of Pharmacy Practice  

Determining mechanisms of antibiotic resistance during chronic microbial lung infection
PI: Sophie Darch, PhD Assistant Professor, Molecular Medicine  

The role of gut microbiota in exacerbating or alleviating immune dysregulation in patients and mouse model of partial RAG deficiency                             
PI: Jolan Walter, MD, PhD, Robert A. Good Endowed Chair, Division of Pediatric Allergy & Immunology  

Probing lipidomic signatures of small extracellular vesicles for cellular origins
PI: Theresa Evans-Nguyen, Associate Professor, Department of Chemistry

In a population of healthy maternal/infant dyads, does the milk microbiome reflect circadian rhythmicity?
PI: Kelley Baumgartel, PhD, RN, Assistant Professor, College of Nursing

Conduct a 16S rRNA profiling analyses to compare fecal microbiome profiles in these uninfected and infected groups of mice who had moderate TBI
PI:  Shyam Mohapatra, PhD, MBA, FAAAI, FNAI, FAIMBE, FAAAS, FASEMFL, USF Health Taneja College of Pharmacy 

Development of a Dietary Intake Mobile App Designed for Older Adults
Yu Sun, PhD, Department of Computer Science and Engineering

2021-2022 Recipients 

2019-2020 Recipient

External Funding Opportunities

Below is a list of external grant opportunities in the field of microbiomes.  They include grants that specifically support microbiome research, as well as those that, while not microbiome-specific, would certainly be applicable.  

If you see a microbiomes-related funding opportunity that is not listed here, please send it to and it will be added to the list. 

(Click on each category to expand.)

  • National Institutes of Health (NIH)

    Resource-Related Research Projects for Development of Animal Models and Related Materials (R24 Clinical Trials Not-Allowed)

    Due Dates: September 25, 2023; January 25, 2024; May 25, 2024
    For more information:

    Microbial-based Cancer Imaging and Therapy - Bugs as Drugs (R01 Clinical Trial Not Allowed)

    Funding Opportunity Announcement (FOA) Number: PAR-22-085
    Due Date:  October 5, 2023, February 5, 2024
    For more information

    Modulating Human Microbiome Function to Enhance Immune Responses Against Cancer (R21 Clinical Trial Not Allowed)

    Funding Opportunity Number: PAR-22-062
    Due Date:  October 16, 2023, February 16, 2024
    For more information:

    Identification and Characterization of Bioactive Microbial Metabolites for Advancing Research on Microbe-Diet-Host Interactions (R01 Clinical Trial Not Allowed) Funding Opportunity

    Announcement (FOA) Number: PAR-21-253
    Due Date: October 19, 2023
    For more information: 

    Research Projects in Physical Sciences-Oncology (U01 Clinical Trial Optional)

    FOA Number: PAR-22-147
    Due Date: November 01, 2023
    Relevance to Microbiomes: “Potential questions to be addressed include, but are not limited to:  How do physical properties of the immune system, host-microbe interactions, or microbiome composition impact cancer complexity and progression? Could these physical properties be used to evaluate early indicators of the disease? How can microbiome frameworks and their complicated system of systems be applied to cancer research to better understand host, cancer cell, and tumor microenvironment interactions in cancer biology.”
    For more information:

    Blueprint Neurotherapeutics Network (BPN): Biologic-based Drug Discovery and Development for Disorders of the Nervous System (U44 Clinical Trial Optional)

    Funding Opportunity Announcement (FOA) Number: PAR-21-233
    Due Dates: February 9, 2024 (Letter of Intent due 30 days prior to due date).
    Relevance to Microbiomes: “This Funding Opportunity Announcement (FOA) supports preclinical discovery and development of potential therapeutic Biotechnology Products and Biologics including, but not limited to, large biologic macromolecules, (e.g., proteins, antibodies, and peptides), gene-based therapies (i.e., oligonucleotide- and viral-based), cell therapies, and novel emerging therapies (e.g., microbial and microbiome therapies).”
    For more information: 


  • National Science Foundation (NSF)

    Plant Biotic Interactions

    Notice Number: NSF 18-590
    Due Date:  Continuous.
    Approximate Funding Amount: $18,500,000 depending on availability of funds$10.5M from NSF for new standard or continuing grant awards, and approximately $8M from USDA/NIFA for new awards. Both estimates depend on availability of appropriations. USDA/NIFA will support projects for up to four years in duration. Although there are no formal upper or lower limits to award amounts, they typically range from $50,000 to $300,000 per year, with durations of two to four years (and five years for CAREER awards). Enactment of additional continuing resolutions or an appropriations act may affect the availability or level of funding for this program.
    For more information: 

    Transitions to Excellence in Molecular and Cellular Biosciences Research (Transitions) 

    Notice Number: NSF 21-508
    Due Date:  Continuous.  
    Anticipated Funding Amount: $6,000,000 Pending availability of funds
    For more information:  

    Physiological and Structural Systems (PSS)

    Due Date: Continuous
    For more information


  • U.S. Department of Energy

    FY 2023 Continuation of Solicitation for the Office of Science Financial Assistance Program - Biological and Environmental Research (BER) - Biological Systems Science

    Due Date: September 30, 2023
    Description: "The major research objectives are to: Determine the molecular and regulatory mechanisms governing genotype to phenotype translation needed to predictively understand genome-scale functional properties of microbes, plants, and microbiomes relevant to BER s research efforts; develop experimental"-omics" capabilities and enabling technologies needed to achieve a dynamic, system-level understanding of cellular and microbiome functions; and develop the knowledgebase, computational infrastructure, and modeling capabilities to advance predictive understanding and design of biological systems for a variety of bioenergy, environmental and synthetic biology applications underpinning a broader bioeconomy. Develop the advanced characterization, measurement and imaging technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes, information crucial for developing an understanding of the impact of various environmental and/or biosystems design impacts on whole cell or community function."
    For more information:

    U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Community Science Program (CSP) Functional Genomics

    Due Date: January 29, 2024
    For more information


  • Department of Defense (DOD)

    NRL Long Range Broad Agency Announcement (BAA) for Basic and Applied Research - Materials Science and Component Technology Directorate Code 6000 - 69-23-01 - Research In Bio/molecular Science And Engineering

    Due Date: September 29, 2023
    Description: "Current research areas include: Systems and synthetic biology, such as genomics, transcriptomics, proteomics, and metabolomics measurements of isolate microorganisms, microbiomes, and/or environmental consortia. Areas of specific interest include bioinformatics and database development for '- omics' data analyses."
    For more information:

    US Army Combat Capabilities Development Command Broad Agency Announcement

    Issued by: Department of Defense
    Due Date(s): Feb 28, 2025
    Funding Opportunity Number: W911QY20R0022
    For more information:


  • Private / Foundations

    Biocodex Microbiota Foundation Grant

    Sponsor: Biocodex
    Due Date: October 1st, 2023
    For more information:

    The American Quarter Horse Foundation (AQHF) Research Grants - Refrigerator Fund for Equine Head Trauma

    Sponsor: American Quarter Horse Association
    Due Date: November 1, 2023
    For more information:

    Investigators in the Pathogenesis of Infectious Disease

    Sponsor: Burroughs Wellcome Fund
    Due dates: November 15, 2023
    For more information:

    American College of Gastroenterology - Clinical Research Award Pilot Projects

    Due Date: December 4, 2023 
    For more information

    American Gastroenterological Association Grants

    Due Date: Varies
    For list of Grants  

    American Society of Transplantation Research Grants

    Due Dates: Varies
    For more information:    

  • Fellowships

    U.S. Department of Agriculture (USDA)- Agricultural Research Service (ARS) Undergraduate Student Internship in Bioinformatics

    Due Date: Applications may be reviewed on a rolling-basis, and this posting will remain open until a qualified candidate is identified.
    Location: A research opportunity in Bioinformatics is available with the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Sustainable Agriculture Systems Laboratory in Beltsville, Maryland.
    For more information:

    U.S. Food and Drug Administration (FDA) Fellowship in Microbiome and Infectious Disease

    Due Date: Applications will be reviewed on a rolling-basis, and this posting will remain open until filled.
    Location: Laboratory of Dr. Paul Carlson in the Office of Vaccines Research and Review (OVRR) at the Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA) in Silver Spring, Maryland
    For more information

    Nutrition and Human Performance Fellowship at the U.S. Army Research Institute of Environmental Medicine (USARIEM)

    Location: Natick, Massachusetts Due Date: Applications are reviewed on an ongoing basis and fellowships will be filled as qualified candidates are identified.
    For more information:

    U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS) Postdoctoral Fellowship in Salmonella Interventions and Antibiotic Resistance

    Due date:  September 29, 2023
    For more information

    U.S. Environmental Protection Agency (EPA) Fellowship on Cardiopulmonary and Behavioral Effects of Climate Change and Living Environment

    Due Date: October 13, 2023
    For more information:

    Environmental Microbiome of the International Space Station - Omics Analyses

    Due date: November 01, 2023
    For more information:

    US Department of Agriculture (USDA), Agricultural Research Service (ARS) SCINet/AI-COE Postdoctoral Fellowship in Using AI to Address Large, Complex Datasets in Microbiome-based Integrated Pest Management

    Due Date: January 05, 2024
    Location: US Department of Agriculture (USDA), Agricultural Research Service (ARS), at the Biological Control of Insects Research Laboratory located in Colombia, Missouri.
    For more information:



  • USDA

    Agriculture and Food Research Initiative - Foundational and Applied Science Program - Crosscutting Programs - Agricultural Microbiomes in Plant Systems and Natural Resources - Equipment Grants

    Due Date: October 05, 2023
    For more information:

    Agriculture and Food Research Initiative - Foundational and Applied Science Program - Crosscutting Programs - AFRI Commodity Board Co-funding Topics

    Due Dates: August 1, 2024
    For more information

    Agriculture and Food Research Initiative - Foundational and Applied Science Program - Food safety, nutrition, and health - Food and Human Health - Seed Grants

    Due Date: August 8, 2024
    For more information: