Progress 06/01/24 to 05/31/25
Outputs
Target Audience: During this reporting period, I reached the following target audiences: Master Gardeners, producers, academic researchers, students, and the general public. Methods for delivering preliminary outcomes of the study included invited lectures at Extension Master Gardener events and research lab meetings, formal classroom instruction, and graduate student training in laboratory and analysis techniques. The reasons for targeting these specific target audience groups are threefold: 1. It is important for people who produce (and consume) fresh fruits and vegetables to understand the drivers of food-associated microbial community assembly and change, as well as potential impacts on the human gut microbiome; 2. Sharing results with the academic research community will help advance the state of knowledge, identify gaps to be filled by future research, and foster collaboration; 3. Teaching undergraduate and graduate students about the study outcomes may inspire them to pursue research on their own and provide them with valuable skills for employment. Changes/Problems:During this reporting period, a no-cost extension was requested as a result of my heavier-than-expected teaching load during the first year of the project. The NCE was granted and I am on track to complete the project by the end of the next reporting period. In addition, the extra time and lower-than-expected sequencing costs (detailed in the previous progress report) has allowed for a small extra scope of work on science communication research, which I believe will be extremely useful in understanding how lay audiences perceive the study outcomes and prioritize future research directions. I am currently applying for IRB exempt determination for an anonymous online survey to be distributed to lay audiences exposed to the study outcomes (e.g., through attending Master Gardener events, receiving participant reports, or reading blog posts). What opportunities for training and professional development has the project provided?Through this project, three graduate students have received training in laboratory techniques and data analysis using R. Several classroom lectures were given, as well as invited talks at lab group meetings, Master Gardener events, and a landscape architecture webinar. How have the results been disseminated to communities of interest?To date, the primary avenues for dissemination have been academic channels and Master Gardener events. As described in the next section, I will seek to share study outcomes with a larger audience once interpretation of the results has been finalized. What do you plan to do during the next reporting period to accomplish the goals?In the next (and final) reporting period, I plan to accomplish the following objectives: - finalize interpretation of the results and publish in a peer-reviewed journal (submit by 30 September to special collection Food Microorganisms and Genomics in journal Microorganisms); - deliver individual reports to study participants; - provide public updates on the project outcomes through blog and social media posts; - present final results at ASSA/CSSA/SSSA conference in Salt Lake City, Utah, in November 2025; - conduct a small pilot study on science communication to evaluate effectiveness of graphic/text communication in individual reports and presentations to general public audiences, as well as to assess audience's change in knowledge and opinions about future research directions; - evaluate overall success of the project by comparing actual outputs to planned outputs from the original proposal's logic model; and - develop a full proposal to follow up on outcomes from this seed grant project, informed by responses from the science communication study.
Impacts
What was accomplished under these goals?
Fresh fruits and vegetables are known to harbor abundant microorganisms, or microbes, both in the field and on the dinner plate. It is also known that the types of microbes present can change dramatically between harvest and consumption, depending on a variety of factors, such as supply chain length and degree of handling and processing. However, despite the potential implications to human health, the difference in microbial community composition between store-bought (long supply chain) and garden-fresh (short supply chain) produce has not previously been characterized. The outcomes of this study will be relevant to everyone who consumes fresh fruits and vegetables, particularly those who grow their own food in backyard gardens and/or purchase fresh local produce from farmers markets and community-supported agriculture programs. The results may also be of interest to food producers, distributors, and others who play a role in the food supply chain. 1. Major activities completed / experiments conducted - 20 out of target 20 participants successfully completed dietary trial and returned fruit/veg and fecal samples - wetlab processing completed for all received samples - bioinformatics and data analysis completed - abstract submitted to Food Microorganisms and Genomics, a special issue of Microorganisms - manuscript in preparation 2. Data collected - lifestyle, health, and diet questionnaire data for all 20 participants - daily fruit/veg intake data for all 20 participants - qPCR data for all 20 participants - shotgun metagenomics data for fruit/veg and fecal samples for all 20 participants 3. Summary statistics and discussion of results. - Average age of participants: 35 years (range: 24--47) - Biological sex of participants: 16 female, 4 male - Ethnicity: all 20 reported "Not Hispanic or Latino" - Race: 19 White, 1 Black or African American - qPCR: 10.1 mean log10 gene copies for fecal samples, 7.5 mean log10 gene copies for produce samples - Shotgun metagenomics: 5,866,419,923 total microbial DNA sequences representing 16,802 unique taxa Interpretation of the results is ongoing. An abstract has been submitted to a peer-reviewed journal and a manuscript is in preparation. I anticipate publication by early spring.
Publications
|
Progress 06/01/23 to 05/31/24
Outputs
Target Audience: Academic researchers Home gardeners and urban farmers Students Changes/Problems:During the 2023-24 school year, I was asked to take on a heavy teaching load (7 courses), due to a severe faculty shortage in my department. As a result, I was not able to commit as much of my FTE to this project as initially planned and, thus, the project is under-budget and behind schedule. To rectify this, I intend to request a no-cost extension (NCE) during the next reporting period. In addition, recruitment for the dietary trial did not achieve the target number of participants in summer 2023, so I am currently recruiting additional participants. Since I will be requesting a NCE, this additional recruitment period is not expected to further impact the study. Another unanticipated change that occurred during the first year of the study was that the Genomics and Cell Characterization Core Facility at University of Oregon offered a new miniaturized library prep service for whole-genome shotgun metagenomics, which decreased the cost of sample processing and may allow for additional participants and samples to be collected. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?I am currently in the process of recruiting additional participants to achieve the target number of participants. Due to the research question and experimental design, the study is restricted to times of the year when fruit and vegetable crops are being harvested. I expect to achieve the target number of participants before October 2024. Analysis of the samples received to date has been largely completed, with the exception of shotgun metagenomics data. Raw shotgun data was received from the sequencing facility in June and I am now processing and analyzing these data. In terms of dissemination and outreach, I plan to share preliminary results at at least one conference during the next reporting period, as well as posting at least 4 blog and/or social media updates. After data analysis has been completed, I will offer participants access to their own personal results. I will also begin writing a manuscript(s) to submit for publication in a peer-reviewed journal.
Impacts
What was accomplished under these goals?
Fresh ready-to-eat supermarket produce undergoes extensive handling and processing steps throughout the lengthy supply chain (Figure 1), and each instance of handling by human workers or contact with processing surfaces and liquids may alter the intrinsic microbiome of fresh vegetables. In fact,dramatic changes in microbial composition have been documented for supermarket produce.On the other hand, garden-fresh produce experiencesan abbreviated route from harvest to the table and likely undergoing much less washing and sanitizing, thus, it may still harbor indigenous plant- and soil- associated microbiota. Despite this potential reservoir, little research has been done to characterize the microbiomeof garden-fresh produce. The outcomes of this research are expected to inform other academic researchers, fruit/vegetable producers, and the general publicabout potentially divergent microbial communities inhabiting garden vs. supermarket produce. While the study will not explore any health outcomes, it will highlight differences in prevalence and abundance of key microorganisms, including potential pathogens and potentially beneficial taxa. ?Major activities completed / experiments conducted; 11 out of target 20 participants successfully completeddietary trial and returned fruit/veg and fecal samples wetlabprocessing completed for all receivedsamples Data collected qPCR data analyzedfor all 11 participants daily fruit/veg intake data analyzed lifestyle, health, and diet questionnaire data analyzed shotgun metagenomics data for fruit/veg and fecal samplesreceived from sequencing facility bioinformatics and data analysis in progress Summary statistics and discussion of results. To date, a total ofover 2.6 billion microbial sequences have been recovered from fecal, produce, and tapwater samples collected by study participants. Of these, 99.67% were ofbacterial origin. Preliminary results showed no difference in alpha diversity of produce from gardens vs supermarkets, nor ofbaseline, treatment A (consumegarden produce), or treatment B (consume supermarket produce)fecal samples. However, taxonomic composition of produce from the two sources does appear divergent.As the experiment has not been completed, there is insufficient data to draw firm conclusions about the differences in diversity or composition between the two sources of fresh fruits and vegetables.
Publications
|