Welcome to the USF Microbiomes Institute

The USF Microbiomes Institute is an initiative to merge and integrate interdisciplinary researchers and departments from the University of South Florida (USF), USF Health, Tampa General Hospital, James A. Haley Veterans' Hospital and Moffitt Cancer Center, with a particular working focus on microbiomes studies in soil, water, plant, animals, food and human health.

The Institute intends to join different departments and colleges, from engineering to business, and create opportunities for transdisciplinary projects with new approaches to microbiome studies.

Composed of several working groups such as Education and Training, Data Analysis, Infrastructures, Core Facilities, and Scientific programs, we integrate academics with industry, promoting partnerships with colleges and departments to share experiences and enhance research and knowledge in the microbiome field.

Annual Town Hall Meeting

Apr 17

Microbiomes Town Hall

Join us at our annual Microbiomes Town Hall.
Registration starts at 9:30 am.
The workshop begins at 10 am.
Parking will be provided.

Free

Town Hall Keynote Speaker

"Microbial-derived small molecules in cancer progression and treatment"

Christian Jobin, PhD

UFHCC Co-leader Immuno-Oncology and Microbiome

Gatorade Professor of Medicine

Department of Medicine

University of Florida

Dr. Jobin is interested in bacteria/host interactions and ensuring innate/immunological responses during health and diseases. The intestine poses an interesting conundrum – it must peacefully cohabit with a sea of commensal bacteria (~100 trillion) and a high load of bacterial products, but swiftly respond to the presence of pathogenic micro-organisms that threaten its integrity. A major clinical consequence of deregulated bacteria/host interaction in the intestine is the development of inflammatory bowel diseases (IBD) and colorectal cancer. Using mice and zebrafish housed in germ-free and gnotobiotic conditions, microbiome techniques (next-generation sequencing, microbial gene mutations, microbial RNA sequence, etc.), Dr. Jobin studies the differential contribution of bacteria in protecting or exacerbating the development of colitis and colorectal cancer. Dr. Jobin has contributed to the understanding of the cellular and molecular mechanisms regulating host response to bacterial colonization and has published numerous papers on innate signaling events taking place in the intestine and how these impact intestinal homeostasis.

Full Agenda

Call for 2024-25 USF-TGH Cancer Institute (TGHCI) Microbiome Joint Pilot Research Award Proposals

The USF-TGHCI Microbiome Joint Pilot Research Awards are intended to enhance and harness the

collaborations among USF and TGH Cancer Institute investigators by attracting new scientific expertise to complement ongoing research, encourage and promote multidisciplinary microbiome research, and support preliminary investigations to attract new extramural microbiome-related funding at both the USF and TGH Cancer Institute.

These awards will support collaborative research between faculty from different colleges/ schools or

departments of USF and TGH. Research topics should focus on the microbiome and its relationship to cancer.

Funds are awarded through a competitive grant application process described in detail below in the full RFP.

This award is intended to invite applications from multi-PI who will conduct bold, imaginative, rigorous, and relevant research transitioning successful funding and peer-reviewed publications. Each grant will be awarded for up to $30,000 ($15,000 for USF and $15,000 for TGH Cancer Institute Investigators) for one year in project-

related direct costs, including appropriate staff salary support and supplies, at least one going to a junior faculty member.

Full RFP

Microbiome Institute Survey

We are putting together an annual progress report for the USF Institute on Microbiomes. This will feature all activities of the Institute, including:

The Microbiome Research Awards
Seminars and Workshops
Research by the microbiome research community

In particular, we urgently need to get all grant applications (including the dollar amount) from you on the microbiome you have submitted, and hopefully obtained, over the past three years.

Once compiled, we will incorporate this information into this report and distribute it to the USF Microbiome community and beyond.

Survey

USF Microbiome Research Award

We are currently accepting applications for the Ignite Award. 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.

Full RFP

Support us

News and Articles

From Diabetes to Dementia: A Gut Microbiome Exploration With Dr Hariom Yadav

Dr. Hariom Yadav was featured on the podcast "The Microbiome Mavericks" on Spotify.

Listen here

USF Tech Tour featuring Dr. Hariom Yadav

On April 2nd, the USF Tech Tour featured Dr. Hariom Yadav, an Associate Professor of Neurosurgery and Brain Repair and Director of the USF Center for Microbiome Research. He joins host Cheryl Abrigo to discuss his technologies investigating how disturbances in the gut microbiome contribute to the risk of dementia and other age-related chronic diseases such as diabetes, cardiovascular disease, cancer, and dementia.

Watch Here

Sea urchin killer spreads to new species, region

A parasite that devastated long-spined sea urchins in the Caribbean and Florida in 2022 has caused another die-off more than 7,000 miles away in the Sea of Oman.

The discovery, led by researchers at the University of South Florida College of Marine Science (USF CMS) and recently published in The ISME Journal, reveals how the spread of a microscopic pathogen threatens sea urchin populations and coral reefs around the world.

“Sea urchins play an important role in reef health by eating algae,” said Isabella Ritchie, a graduate student at USF CMS and first author of the new study. “When urchins and other herbivores die off, algae can take over and prevent coral from having access to light. A healthy reef tends to have a lot of herbivores.”

Health Headlines: Diet may reduce risk of dementia

More than six million people in the US, 65 and older, have dementia. By 2050, that number is expected to double to nearly 13 million. But a series of new studies reveals you may be able to reduce your dementia risk with the foods you choose to eat.

You are what you eat.

Hariom Yadav, PhD, Director USF Center for Microbiome Research says, “The gut influences very heavily the whole body physiology.”

Do you really want that hamburger? Exploring the links between diet, gut health and diabetes

Countless people in the United States suffer from a condition called “leaky gut,’’ where the lining of the intestines becomes porous enough to allow toxins to seep through it and into the bloodstream.

Many are unaware of their condition, or that it can lead to serious health problems, such as chronic inflammation, type 2 diabetes, heart disease, dementia and even some types of cancer. The condition also can cause a variety of unpleasant gastrointestinal syndromes, such as indigestion, gas, bloating, abdominal pain and diarrhea.

In a new paper published in Gut, a leading high-impact international journal in gastroenterology and hepatology, USF Health researchers describe how the right balance of bacteria can deter leaky gut – and how the wrong mix can threaten a person’s health.

Tracing the link between aging microbes and the brain

Hariom Yadav, Ph.D., has a gut feeling about how bacteria in a person’s digestive tract can affect their mental health.

In a new study, Dr. Yadav and a team of researchers from around the United States say that age-related abnormalities in gut microbiota – the collection of bacteria, viruses, and other cellular organisms -- are associated with cognitive decline, depression, and anxiety. They hope their findings could one day lead to improved treatments in these critical areas.

Nominees National Academy of Inventors for 2024

Seven USF faculty have been named senior members of the National Academy of Inventors for 2024. Congratulations to Professors Redwan Alqasemi, Paula Bickford, Sarina Ergas, Shri Goyal, Rasim Guldiken, Hariom Yadav and Tansel Yucelen!

International Conference on "Microbiomes, Biodiversity, and Their Impact on Global and One Health”

On October 16th -18th 2023 in Annecy, France, the University of South Florida, the Principality of Monaco (Scientific Center of Monaco and Fondation Prince Albert II), the Fondation Mérieux, and the Global Virus Network brought together some thirty experts from a wide range of backgrounds: members of intergovernmental organizations (WHO, FAO) and international initiatives (Lancet Eat), experts in the microbial ecology of oceans, soils, plants, and people, specialists in nutrition and human health and its relationship within microbiomes and environmentally friendly agricultural practices, and industrial players that develop solutions as part of an eco-responsible agri-food chain. For the first time, it has enabled a genuine dialogue to be established between players from these different communities around a common issue - the characterization of microbiomes - and to highlight not only shared issues and challenges on this subject but also integrated and concrete solutions based on a better understanding of microbiomes for the implementation of eco-responsible agricultural and aquacultural practices and nutritional and therapeutic approaches beneficial to our health.

Learn More

Funding Opportunities

Government Grants

National Institutes of Health (NIH)

Due Date: May 25, 2024

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: July 15, 2024. LOI is due 30 days before the application 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).”

Investigator Initiated Clinical Trials of Complementary and Integrative Interventions Delivered Remotely or via mHealth (R01 Clinical Trial Required)

Funding Opportunity Number: PAR-24-086

Due Date: June 20, 2024

Relevance to Microbiomes: High program priority: Studies to examine the effects of prebiotics/probiotics and other natural products on gut microbiome-brain interactions. Of particular interest are studies of prebiotics/probiotics for depression, anxiety disorders, irritable bowel syndrome (IBS), or chronic pain.

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

Funding Opportunity Number: PAR-22-062

Due Date: June 16, 2024

Understanding the Basic Mechanisms of Immune-related Adverse Events (irAEs) in Cancer Immunotherapy

Notice Number: NOT-CA-22-063

Due Date: Varies; please see full announcement.

Relevance to Microbiomes: Specific Areas of Research Interest to NCI include: Investigating the role of the microbiome in the generation or prevention of irAEs resulting from cancer immunotherapies. Specific Areas of Research Interest to NIAID include: Identifying predictive biomarkers for the onset of irAEs (e.g., genetics, epigenetics, microbiome, and overall immune status).

Pilot Studies of Biological, Behavioral and Social Mechanisms Contributing to HIV Pathogenesis Within the Mission of the NIDDK (R21 Clinical Trial Not Allowed)

FOA Number: PAR-21-062

Due Date: Standard AIDS dates apply. 

Relevance to Microbiomes: “The scope of this FOA includes but is not limited to: The impact of HIV or its treatment on the gastrointestinal or penile microbiome, pathogenic enteric microbes, male genital tract infections, or co-infection with hepatitis viruses.”

Understanding the Basic Mechanisms of Immune-related Adverse Events (irAEs) in Cancer Immunotherapy

Notice Number: NOT-CA-22-063

Due Date: July 05, 2024

Description: Areas of interest: Investigating the role of the microbiome in the generation or prevention of irAEs resulting from cancer immunotherapies; Identifying predictive biomarkers for the onset of irAEs (e.g., genetics, epigenetics, microbiome, and overall immune status).

Innovation for HIV Vaccine Discovery (R01 Clinical Trial Not Allowed)

Notice Number: PAR-23-169

Due Date: August 02, 2024

Description: Areas of interest include: Exploring the impact of the host microbiome on vaccine-induced immunity and efficacy

Intervention Research to Improve Native American Health (R21 Clinical Trials Optional)

Notice Number: PAR-23-299

Due Date: October 21, 2024

NIH Notice of Special Interest (NOSI)

Notice of Special Interest (NOSI): Chronic Inflammation of the Oral Cavity - An Agent for Oral Mucosal Disease

Notice number: NOT-DE-23-007

Due Date: This notice applies to due dates on or after February 5, 202 4, and subsequent receipt dates through September 7, 2026.

Notice of Special Interest (NOSI): Investigations on Inborn Errors of Immunity/Primary Immunodeficiencies

Notice Number: NOT-AI-21-032

Due Date: This notice applies to due dates on or after June 5, 2021, and subsequent receipt dates through May 7, 2024.

Relevance to Microbiomes: “Research areas supported by this NOSI include, but are NOT limited to…Investigating the role of gut microbiome in the pathogenesis of inborn errors of immunity.”

Notice of Special Interest (NOSI): Capturing Complexity in the Molecular and Cellular Mechanisms Involved in the Etiology of Alzheimer's Disease

Relevance to Microbiomes: Areas of high program relevance include, but are not limited to, the following: Molecular mechanisms by which peripheral systems (e.g., immune, metabolic, microbiome) interact with the brain during aging and the impact of this interaction on the initiation and progression of neurodegeneration in AD.

Due Date: This notice applies to due dates on or after March 11, 2022, and subsequent receipt dates through November 13, 2024.

Notice of Special Interest (NOSI): Opportunities for Research in Epidemiology of Alzheimer's Disease and Alzheimer's Disease-Related Dementias (AD/ADRD) and Cognitive Resilience

Notice Number:  NOT-AG-21-045

Due Date: This notice applies to due dates on or after March 11, 2022 and subsequent receipt dates through November 13, 2024.

Relevance to Microbiomes: “Enabling precision medicine for AD/ADRD through deep phenotyping: The precision-medicine approach presents new opportunities for understanding the behavioral, social, environmental, and molecular determinants of AD/ADRD risk and cognitive resilience in diverse populations and at the level of the individual. This NOSI invites applications that will enhance the potential of community-based cohort studies to enable precision medicine for AD/ADRD by, for example: expanding the types of cross-sectional and longitudinal ante- and post-mortem-biospecimen data collection needed to generate multiple layers of “omics” data; incorporating dense molecular endophenotyping (e.g., genomic, epigenomic, proteomic, metabolomic, and microbiomic)..”

Notice of Special Interest (NOSI): Stimulating Research to Understand and Address Hunger, Food and Nutrition Insecurity

Due Date: November 29, 2024

Description: "The purpose of this NOSI is to encourage research on the efficacy of interventions that address nutrition security and the mechanisms of food insecurity on a variety of health outcomes."

Notice of Special Interest (NOSI): Leveraging Microbial Exposure for Improving Mouse Models of Human Immunity

Notice Number: NOT-AI-21-072

Expiration Date: January 8, 2025

Notice of Special Interest (NOSI): The Functional Oral Microbiome

Due Date: September 7, 2025 (Notice expiration date).

Notice of Special Interest (NOSI): Addressing the Etiology of Health Disparities and Health Advantages Among Immigrant Populations

Notice Number: NOT-MD-23-002

Expiration Date: June 06, 2026

National Science Foundation (NSF)

Dear Colleague Letter: Future Proofing Plants to a Changing Climate

Notice Number: NSF 23-096

Due Date: Continuous

Plant Biotic Interactions

Notice Number: NSF 18-590

Due Date: Continuous

Relevance to Microbiomes: “Research may focus on the biology of the plant host, its pathogens, pests or symbionts, interactions among these, or on the function of plant-associated microbiomes.”

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

Physiological and Structural Systems (PSS)

Due Date: Continuous

Department of Energy

CSP Functional Genomics

Due Date: January 30, 2025

USDA

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

Agriculture and Food Research Initiative - Foundational and Applied Science Program - Plant Health and Production and Plant Products - Physiology of Agricultural Plants - Standard Grants

Due Date: August 22, 2024

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 03, 2024

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

Due Dates: August 1, 2024

NGOs / Private Sources

Call for national project USA - Biocodex Microbiota Foundation 2024

Due Date: October 1, 2024

Description: Gut Microbiota in human health and disease focusing on groundbreaking areas of research such as circadian rhythms, neurological conditions, metabolic disorders, and oncology

American Gastroenterological Association Grants

Due Date: Varies

Description: “The AGA Research Foundation provides over $2 million annually to spur discoveries in gastroenterology and hepatology.”

American Society of Transplantation Research Grants

Due Dates: Varies

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.

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

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.

General Resources

USF Microbiome Institute – Grants

Funding Resources (USF Sponsored Research)

Federal Government grants search: https://www.grants.gov/web/grants

About Funding at NSF: https://nsf.gov/funding/aboutfunding.jsp

Grants and Funding at NIH: https://www.nih.gov/grants-funding

Funding Search (Office of Research and Scholarship):

https://www.usf.edu/arts-sciences/research-scholarship/funding-search/

Faculty Insight: https://www.usf.edu/ods/data-tools/faculty_insight.aspx