All Harvard NIEHS Center members are eligible to apply for pilot project funds. Other faculty or research scientist level researchers may apply in collaboration with a Center member co-investigator. Applications are accepted from Harvard Research Associates or Fellows working under the supervision of Center faculty, but the role of the sponsoring faculty member must be specified. Doctoral students are not eligible for pilot project support.

Requests for Pilot Project applications are announced twice a year via postings at the Harvard T.H. Chan School of Public Health, email, and on our website. Due dates are usually the first Friday of March and October (can vary).

Funding decisions are typically announced within 6-8 weeks from the application deadline.

Applications follow an abbreviated NIH structure, including a narrative section (2-3 single-spaced pages) with background, specific aims, experimental protocols; a brief budget and justification; and an NIH format biosketch for the principal investigator and co-investigators.

Email completed Application Form with biosketch(es) to niehsctr@hsph.harvard.edu (cc sunninayar@hsph.harvard.edu) and fill out the Qualtrics form.

• Total requested costs for a one-year project period may not exceed $30,000 total costs.
  • Subcontracts are allowed, however, if the sub-institution requires indirect costs, it will be included in the $30K total.
• The PI is required to have a minimum of 1% effort devoted to project.
  • PI Salary between 1-3% commensurate with effort is allowable.
  • The NIH Salary cap should be applied if faculty salary is over the cap.
• In some cases, postdoc salary or technical support salary may be appropriate (e.g., biostatistical support).
• The budget may include funds for supplies and other appropriate costs directly related to the project.
• Travel costs are not supported except those essential to carry out the project.
• Unallowable costs include: graduate student stipends, publication costs/page fees, food, and costs usually allocated to overhead (e.g., data storage).

No, clinical trials are not allowed under the terms of the award.

Funds are awarded for a period of one year. A one-year extension may be requested but carry forward is not guaranteed.  To request carry forward, fill out this Pilot Project No Cost Extension Request form.

Each application is reviewed by three or more reviewers, at least one of whom is not a Harvard Chan NIEHS Center member. Evaluation criteria include:

1. Innovation
2. Study Design
3. Project team
4. Potential for future funding
5. Relevance to the Harvard NIEHS Center mission
6. Potential for stimulating collaborative research

The Pilot Project Review Committee meets to consider the reviews, rank the proposals and make funding decisions.

Funding is determined by the Review Committee ratings, and the availability of funds in a particular cycle. Funding decisions are provided to the applicants along with a summary of comments from the internal and external reviewers. Applicants may be asked to address critical issues before final approval. Unfunded applicants are encouraged to consider reviewer feedback and re-apply during the following funding cycle. Unfunded projects are allowed one resubmission.

Funding success rate can vary with the quality of the proposals and the availability of funds. Over the past several years, the funding rate has been approximately 30% with the average award around $24,000. Click here to see a list of previously funded Pilot Projects.

Funding recipients will be contacted periodically by the Center Administrator to monitor progress. At the completion of the project, the investigator will submit to the Center Director a short summary of the project and its findings, publications, and applications for independent funding that have resulted from the pilot project. Investigators may be asked to present their work at a Center-sponsored event, such as at an External Advisory Board meeting or the annual retreat. Recipients will be expected to notify Sarah Unninayar of any publications, press, grant applications or other outcomes related to the pilot funding, and to be responsive to requests for such information annually for Center progress reports.

Investigators must acknowledge support Center support with a statement that the study “was supported in part by a Pilot Project grant from the Harvard Chan NIEHS Center for Environmental Health (P30 ES000002).”

Pilot projects that involve work outside of the US are subject to approval by the NIEHS and the US State Department. This includes use of samples previously collected outside the US. Applications for NIEHS/State Department approval include a study description form, detailed budget and justification, and copies of relevant approvals (IRB, etc). Applications for foreign clearance will be submitted to NIEHS/State Department by the Center Administrator after all other approvals (IRB, IACUC) and subcontract documents are in order, and may take several weeks or longer to obtain. Applicants should plan accordingly.

Please download the appropriate approval form here for projects that involve:

• Work outside the US: Foreign Component Approval Application
• Use of samples previously collected outside the US: Foreign Component Approval Application-Samples

Growing evidence supports a link between gut microbiome dysbiosis and adverse mental states such as depression, anxiety, and other stress-related conditions. However, much less is known about how the gut microbiome relates to positive emotional well-being. Understanding this relationship could help explain the well-established connection between emotional well-being and health and provide further support for the gut-brain axis. Previous studies have been limited by small sample sizes and low-resolution microbiome profiling methods. Here, we analyzed whole-metagenome shotgun sequencing data from 2,019 stool samples collected from women in the Nurses’ Health Study II between 2019 and 2022 to investigate associations between the gut microbiome and optimism. Optimism was measured in 2017 using the validated Life Orientation Test–Revised (LOT-R). We first evaluated overall microbial diversity and community composition across optimism levels and then assessed associations of microbial species and pathways with optimism while adjusting for technical factors and relevant host covariates. We observed a modest increase in gut microbial alpha diversity with higher optimism levels. After correction for technical batch effects, overall gut microbiome composition remained significantly associated with optimism. The gut microbiome composition was also strongly influenced by host factors, including body mass index, diet, and chronic disease status. After adjustment for these host factors, 22 microbial species and 16 microbial pathways were associated with optimism at an exploratory false discovery threshold (adjusted p-values < 0.2). Several of these associations were biologically notable and supported by recent literature. For example, microbes associated with higher optimism were enriched in progestin-related functions and in pathways involved in queuosine and UMP biosynthesis. These findings suggest that gut microbial metabolism may represent an underappreciated mechanism linking the gut microbiome to optimism. This work provides a large-scale, population-based framework for studying positive emotional well-being through the lens of metagenomics and may help guide future mechanistic studies.

Oropharyngeal upper respiratory tract (URT) infections are a common complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT), yet it remains poorly understood how the oropharyngeal URT microbiome contributes to clinical outcomes. In a prospective cohort of 156 recipients, we longitudinally profiled oropharyngeal metagenomes alongside antibiotic exposure and immune profiles. High-risk antibiotics were associated with depletion of endogenous microbes in favor of pathogen dominance, including Enterococcus faecium and Burkholderia cenocepacia. Mediation analysis linked high-risk antibiotic exposure specifically to loss of Prevotella melaninogenica, a modulator of CD8⁺ effector/memory T cells, whose carriage correlated with improved progression-free survival. We identified five reproducible oropharyngeal URT community types, including a newly emerged post-HSCT Burkholderiaceae-enriched cluster that was linked to adverse aGvHD event. A classifier integrating microbial and immune features improved progression prediction in patients with low antibiotic exposure. These findings provide a systematic characterization of the URT microbiome and highlight it as a potential biomarker of HSCT outcomes.

Background: The temporal dynamics of the gut microbiome and its associated factors remain poorly understood.
Methods: We analyzed 3,466 shotgun metagenomes that were repeatedly collected over weeks to years in four cohorts: 213 men from the Men’s Lifestyle Validation Study (MLVS, interval: 6 months), 306 women from the Mind-Body Study (MBS, interval: 6 months), 90 women from the Microbiome Among Nurses Study (Micro-N, interval: 3 years), and 130 participants from the Human Microbiome Project 2 (HMP2, interval: 2-52 weeks). Diet was assessed via food frequency questionnaires, while lifestyle and clinical information were collected by questionnaires administered before or at stool collection. Gut microbiomes were profiled for taxonomy and functions using MetaPhlAn4 and HUMAnN4, respectively. Temporal stability of the gut microbiome was assessed by the within-individual Bray-Curtis (BC) distance between repeated samples over time. Using 10-fold cross-validation Random Forest models, we examined, within each cohort, the variation in species- and pathway-level BC distances explained by dietary (up to 37 food groups, 3 dietary patterns, and fiber intake) and non-dietary factors (lifestyle, medications, and stool-related factors), as well as baseline microbial features.
Results: Overall, collection timepoint explained a minimal (0.2–0.5%) variation in the BC of the microbial compositions (detected species number range: 395–423) and pathways (355–443). Although within-individual BC distances increased with longer time intervals, they remained substantially lower than between-individual distances for both species and pathways (Species BC for 3-year interval, mean: 0.47 vs. 0.73). Within-individual pathways showed higher stability than species. Across cohorts, dietary factors, non-dietary factors, microbial species, and functional pathways accounted for 9.0–16.1%, 11.8–29.0%, 9.4–18.2%, and 4.1–32.3% of the variations in the within-individual species-level BC, respectively. For pathway-level BC, these factors explained 5.9–26.9%, 16.9–21.8%, 7.8–22.6%, 5.2–41.6% of the variation, respectively. No factor consistently predicted within-individual BC distances across all four cohorts.
Conclusions: The gut microbiome is relatively stable in epidemiologic settings, providing important context for future population-based research using fecal microbiome data. The overall associations of dietary and lifestyle factors with microbiome stability were weak and inconsistent.

Distinguishing viable from non-viable microbes remains a major hurdle in microbiome research, limiting our ability to fully understand microbial community structure, function, and transmission. Microbial viability is critical for interpreting the biological and ecological roles of microbiomes, as only living microbes actively participate in processes such as metabolism, signaling, and host interactions. Existing methods, such as chemical-based viability assays and 16S rRNA transcript detection, have proven suboptimal in complex communities, while shotgun metagenomics and metatranscriptomics, though informative, are often prohibitively expensive and computationally demanding. To address these limitations, we are developing a novel, high-throughput viability assessment approach based on sequencing optimized marker gene transcripts.

Our method combines rational marker gene selection, in silico primer design, and amplicon sequencing to enable precise, scalable differentiation of actively transcribing microbes within diverse communities. We have constructed and evaluated a marker gene database, designed candidate primers, and established a marker gene amplicon-sequencing protocol using paired metagenomic and metatranscriptomic datasets. We have further tested this approach in synthetic microbial communities as well as realistic human-associated and built environment samples. In synthetic communities, the marker gene-based method accurately profiled community composition in DNA samples and successfully identified active microbial members in RNA-derived cDNA samples, supporting its potential for viability-aware microbiome profiling. The protocol is now close to finalization, with ongoing efforts focused on updating the marker gene database, further refining marker gene coverage, and implementing a finalized bench protocol for improved robustness and practical use. Once established, this workflow will offer an accessible, culture-independent solution for microbiome viability profiling. This approach has broad implications for advancing microbiome-based diagnostics, therapeutic development, and environmental surveillance by providing a much-needed tool to quantify the active, functional members of microbial communities.