Microbiome research — NIH Funding Overview
Reviewed by Dr. Meng ZhaoLast reviewed June 9, 2026Data refreshed June 9, 2026Editorial standards
Microbiome research at NIH continues to mature beyond the original Human Microbiome Project. Active areas include the gut-brain axis, microbiome-immune interactions, oral and vaginal microbiomes, fecal microbiota transplantation, and microbiome-targeted therapeutics. Multiple ICs fund work depending on disease focus.
Funding snapshot
Award data on this page reflects a snapshot of NIH RePORTER records last refreshed on June 9, 2026. For live numbers, use the interactive trends view.
Why this matters now
Microbiome science has translated into FDA-approved therapeutics (e.g., Vowst, Rebyota for recurrent C. difficile in 2022–23) and ongoing trials in IBD, immune-mediated disease, and oncology immunotherapy response. NIH funding now emphasizes mechanistic and translational work over census-style cataloging.
How NIH funds this area
Mechanisms span R01, R21, U01, U19, and Common Fund initiatives. NIDDK, NIAID, NCI, and NHLBI are major funders depending on disease scope. Data below covers all NIH awards mentioning microbiome in title, abstract, or terms.
How to use this funding brief
Use this page to determine whether recent awards show durable mechanistic or translational momentum rather than another descriptive sequencing wave. Narrow by body site, disease, and intervention type before drawing conclusions from the broad microbiome total.
Official source: NIH Common Fund: Human Microbiome research
Search tactics
- Search "gut microbiome", "oral microbiome", or "vaginal microbiome" for site-specific research.
- For therapeutic applications, search "fecal microbiota transplantation" or "live biotherapeutic".
- Microbiome-immunotherapy intersection (NCI funding) has grown rapidly post-2020.
What the data shows
- Funding peaked in FY2025 at $1.5B. The FY2025 total of $1.5B is +25% versus FY2021.
- The number of awards fell about 7% in FY2025 even as total dollars grew — funding is concentrating in fewer, larger awards.
- About 86% of FY2026 dollars so far are renewals and continuations. Mid-year snapshots overweight renewals because non-competing continuations are issued early in the fiscal year, but the share still indicates how much of the portfolio is committed before new applications compete.
- The average FY2025 award was $702K, and R01 was the most common mechanism in the recent window.
Editorial read
Microbiome funding grew about 25% from FY2021 to a FY2025 peak, but the more useful signal is qualitative: recent awards skew toward mechanistic and interventional designs — engineered consortia, defined communities, microbiome-derived therapeutics — rather than the descriptive sequencing surveys that built the field. Proposals framed as another association study face a much higher bar than the totals suggest.
Yearly NIH Awards for Microbiome research
Counts and total funding per fiscal year from NIH RePORTER. Recent fiscal years may understate final totals because of reporting lag.
| Fiscal Year | Project Count | Total Funding | Avg Award |
|---|---|---|---|
| FY2021 | 1,973 | $1,205,509,055 | $611,003 |
| FY2022 | 2,123 | $1,366,718,352 | $643,767 |
| FY2023 | 2,221 | $1,402,344,546 | $631,402 |
| FY2024 | 2,308 | $1,466,880,966 | $635,564 |
| FY2025 | 2,148 | $1,508,064,363 | $702,078 |
| FY2026 | 837 | $510,132,680 | $609,478 |
Open the full interactive trends view for Microbiome research →
Top NIH Institutes (last 90 days)
Which NIH institutes funded the most Microbiome projects in the most recent 90-day window.
| Institute | Awards (90d) | Funding (90d) |
|---|---|---|
| NIH | 477 | $301,305,860 |
| AHRQ | 2 | $986,606 |
| VA | 7 | $0 |
Common Activity Codes (last 90 days)
Which grant mechanisms (R01, R21, U01, P30, etc.) appeared most often for Microbiome in the recent period.
Most Active Institutions (last 90 days)
Universities and research organizations with the most Microbiome awards in the most recent 90-day window.
- UNIVERSITY OF CALIFORNIA, SAN DIEGO — 15 awards
- STANFORD UNIVERSITY — 14 awards
- UNIV OF NORTH CAROLINA CHAPEL HILL — 14 awards
- UNIVERSITY OF COLORADO DENVER — 11 awards
- WASHINGTON UNIVERSITY — 11 awards
- UNIVERSITY OF WISCONSIN-MADISON — 10 awards
- MASSACHUSETTS GENERAL HOSPITAL — 10 awards
- DUKE UNIVERSITY — 9 awards
Recently Awarded Microbiome research Grants
Twelve most recent awards mentioning Microbiome, drawn from NIH RePORTER. Click through to Find PIs for the full investigator search.
CRCNS: Repurposing Transformers to Characterize Gut Microbiome & Aging Brain Axis
5R01AG092220-03Vikas Singh · UNIVERSITY OF WISCONSIN-MADISON, WI · $369,360 · awarded Jun 5, 2026 · R01For debilitating neurodegenerative diseases such as Alzheimer’s disease (AD), some drugs have been approved but only offer a modest attenuation of cognitive decline. There is a need to better understand the role of modifiable risk factors which could decrease the risk of AD and other types of dementia. The human gut microbiome–comprising of microbes and…
Host and microbial risk factors of oral thrush in cancer patients receiving chemotherapy
5R01DE032131-05Patricia Diaz · STATE UNIVERSITY OF NEW YORK AT BUFFALO, NY · $656,284 · awarded Jun 5, 2026 · R01SUMMARY The factors that underline susceptibility to oropharyngeal candidiasis (OPC; thrush) caused by Candida albicans in different populations are not well understood. In individuals with specific monogenic disorders, OPC susceptibility is dictated by defects in mucosal immune defenses and/or epithelial barrier function. In cancer patients undergoing…
Development of methods for robust gene integration into native gut E. coli
1R21AI194932-01A1Amir Zarrinpar · UNIVERSITY OF CALIFORNIA, SAN DIEGO, CA · $438,625 · awarded Jun 5, 2026 · R21ABSTRACT The objective of this proposal is to develop conjugative methods for rapidly and reliably integrating genes into diverse native bacteria isolates from both mice and humans. This will enable the creation of engineered native bacteria (ENBs) which can be used to study the gut microbiome and develop new therapeutics for chronic diseases. Compared to…
Novel Reengineered Microbiome-based Biologic Therapy to Treat Cognitive and Behavioral Symptoms of Alzheimer's Disease and Related Dementias
5U01AG074960-05Anumantha Kanthasamy · UNIVERSITY OF GEORGIA, GA · $1,473,573 · awarded Jun 5, 2026 · U01Abstract Our early-stage ADDP proposal aims to develop a novel genetically engineered bacterial biologic to treat the most common early symptoms of Alzheimer's disease (AD), including cognitive impairment and other neuropsychological symptoms, such as anxiety and depression. This debilitating disease imposes a huge emotional, social and financial burden on…
Vaginal estradiol versus moisturizer to improve postmenopausal vaginal aging symptoms, dysbiosis and markers of HIV latency reversal in menopausal women living with HIV
1R01AG102277-01Kerry Murphy · ALBERT EINSTEIN COLLEGE OF MEDICINE, NY · $706,734 · awarded Jun 5, 2026 · R01Women with HIV (WWH) are living longer and experiencing menopause, which often occurs earlier than in women without HIV (HIV-), reflecting an accelerated aging phenotype. The genitourinary syndrome of menopause (GSM) affects approximately 50% of menopausal women but fewer than 25% receive treatment. This is particularly concerning for WWH as untreated GSM…
Interactions between the Gut Microbiome, Intestinal Development and Metabolic Health after Fetal Growth Restriction
5K08DK139411-02Stephanie Gilley · UNIVERSITY OF COLORADO DENVER, CO · $129,510 · awarded Jun 4, 2026 · K08PROJECT SUMMARY/ABSTRACT Fetal growth restriction (FGR) impacts 10-20% of pregnancies worldwide and increases the offspring’s risk for later development of obesity and type 2 diabetes due to incompletely understood mechanisms. The focus of this proposal is the nexus of intestinal development and gut microbiome establishment. Gut microbial composition…
Genetic and Microbiome Control of Addiction-like Behaviors in Mice
1U01DA064597-01Jason Bubier · JACKSON LABORATORY, ME · $805,077 · awarded Jun 3, 2026 · U01PROJECT SUMMARY The research proposal addresses the urgent need for predictive biomarkers and pharmacological treatments for cocaine use disorder (CUD), a highly heritable disease affecting millions worldwide. Despite advances in understanding the genetic, cellular, and circuit mechanisms of CUD, effective treatments remain elusive. The proposal highlights…
Role of Gut Microbiome in Smoking Induced Promotion of Pancreatic Cancer
5I01CX002478-02VIKAS DUDEJA · BIRMINGHAM VA MEDICAL CENTER, AL · awarded Jun 3, 2026 · I01Project Summary Pancreatic cancer (PDAC) is the 3rd most common cause of cancer-related mortality in the US. Our veterans and military personnel bear significant brunt of this disease. One of the major obstacles in devising effective treatment strategies against PDAC is the incomplete understanding of its pathogenesis. For instance, smoking is one of the…
Development of Methodologies to Reveal the Role of the Blood Microbiome in the Gut-Lung Axis
5R00HL163519-04Zheng Sun · BRIGHAM AND WOMEN'S HOSPITAL, MA · $249,000 · awarded Jun 3, 2026 · R00Project Summary/Abstract Asthma is one of the most common chronic respiratory diseases worldwide. Microbial dysbiosis in the gut and lungs has increasingly been associated with the incidence and severity of asthma, indicating the potential of the microbiome to be a determinant factor in asthma pathogenesis. However, as the most likely connection between the…
Cross-domain interactions: archaea-bacterial syntrophy in digestive health
1R01DK147125-01Zhe Lyu · NORTH CAROLINA STATE UNIVERSITY RALEIGH, NC · $738,169 · awarded Jun 3, 2026 · R01Abstract While much of the human microbiome research is focused on bacteria, one of the most prevalent yet underappreciated components of the human microbiome is the methanogenic archaea (methanogens). They catalyze the unique methanogenesis metabolism responsible for methane production in the human body. About 1/3 of the healthy adults are breath methane…
Genetic determinants of interbacterial competition during host colonization
5R35GM137886-07Alecia Septer · UNIV OF NORTH CAROLINA CHAPEL HILL, NC · $427,625 · awarded Jun 3, 2026 · R35Project Summary The biological functions of microbiomes are critical to human health. Perturbations of these microbiomes can lead to damaging consequences including improper host development and increased susceptibility to infectious disease. Competitive interactions among microbial populations are predicted to influence the structure and function of…
Determinants of colonization for commensal skin bacteria
5R01AR084097-02Tami Lieberman · MASSACHUSETTS INSTITUTE OF TECHNOLOGY, MA · $442,027 · awarded Jun 3, 2026 · R01Abstract / Project Summary Microbiome-based therapies have untapped potential to prevent infection and treat disease—augmentation of the microbiome might one day promote colonization resistance against pathogens, treat inflammation, and provide therapeutic metabolites. The grand challenge facing microbiome-based therapies is the unpredictability of…
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