Frequently Asked Questions


1 What is the Garden-Fresh Foods (GFF) study?

GFF is a pilot study to explore what types of microbes are present on garden-fresh versus store-bought fruits and vegetables, as well as how they might affect the human gut microbiome.

2 Who is running the study?

Dr. Gwynne Mhuireach (University of Oregon) is running the study with funding from the USDA National Institute of Food and Agriculture.

3 Who can participate in the study?

Enrollment is open to healthy English-speaking adults between the ages of 18–45 living in Lane or Linn County, whose food gardens produce enough fruits and vegetables to satisfy the USDA recommendations for one week, and who are willing to perform all procedures and activities involved with the study.

4 We get a CSA or purchase produce at a farmers market. Can we participate?

Unfortunately, no. This is a pilot study intended to compare garden-fresh versus supermarket produce, because we expect that there is a substantial difference in their respective microbial inhabitants. Produce from a CSA or farmers market likely falls somewhere in between and, thus, would muddy the results. If this project is successful, we do plan to follow-up with a larger study that will include CSA and farmers market produce.

5 Are there any exclusion criteria?

Yes. A variety of factors may influence the gut microbiome. Therefore, to limit the number of non-dietary variables, the following criteria will be cause for exclusion from the study:

  • Body mass index (BMI) greater than or equal to 35 or less than or equal to 18.
  • Age under 18 or over 45.
  • Female who is pregnant or lactating.
  • Irregular bowel movements and/or stool consistency.
  • Plans to travel or move residences during the study period (August–October 2023).
  • Unable to speak, read, and write English.
  • Use of any of the following drugs within the last 6 months:
    • Systemic antibiotics, antifungals, antivirals or antiparasitics (intravenous, intramuscular, or oral);
    • Oral, intravenous, intramuscular, nasal or inhaled corticosteroids;
    • Cytokines;
    • Methotrexate or immunosuppressive cytotoxic agents;
    • Large doses of commercial probiotics consumed (greater than or equal to 108 cfu or organisms per day) – includes tablets, capsules, lozenges, chewing gum or powders in which probiotic is a primary component. Ordinary dietary components such as fermented beverages/milks, yogurts, foods do not apply.
  • Acute disease at the time of enrollment.
  • History of cancer except for squamous or basal cell carcinomas of the skin that have been medically managed by local excision.
  • Unstable dietary history as defined by major changes in diet during the previous month, where the subject has eliminated or significantly increased a major food group in the diet.
  • Recent history of chronic alcohol consumption defined as more than five 1.5-ounce servings of 80 proof distilled spirits, five 12-ounce servings of beer or five 5-ounce servings of wine per day.
  • Any confirmed or suspected condition/state of immunosuppression or immunodeficiency (primary or acquired) including HIV infection.
  • Major surgery of the GI tract, with the exception of cholecystectomy and appendectomy, in the past five years. Any major bowel resection at any time.
  • History of active uncontrolled gastrointestinal disorders or diseases including:
    • Inflammatory bowel disease (IBD) including ulcerative colitis (mild-moderate-severe), Crohn’s disease (mild-moderate-severe), or indeterminate colitis;
    • Irritable bowel syndrome (IBS) (moderate-severe);
    • Persistent, infectious gastroenteritis, colitis or gastritis, persistent or chronic diarrhea of unknown etiology, Clostridium difficile infection (recurrent) or Helicobacter pylori infection (untreated);
    • Chronic constipation.

6 If I participate in this study, what will I have to do?

If you participate, you will be asked to undergo two diet interventions, each lasting 1 week. In one of the two intervention phases, you will be asked to eat the USDA-recommended amount of fruits and vegetables (based on BMI-adjusted caloric intake) with all of the produce sourced from your backyard or school/community garden. In the other intervention phase, you will be asked to eat the same amount and types of fruits and vegetables, but sourcing them from a local supermarket. Each day during both phases, you will fill out a Daily Fruit & Vegetable Log and collect small samples of all the fruits and vegetables you eat. Participants will also collect daily stool (fecal) samples using a special collection kit for the duration of each diet intervention, as well as two days before. In addition, you will be asked to fill out a Lifestyle, Health, & Diet Questionnaire, collect one sample of your tapwater, and return all collected samples back to the research team at University of Oregon.

7 Will I be paid for participating in this research?

Yes. Participants will receive $50 at the beginning of the study, $50 upon completion, and a $75 allowance to purchase one week’s worth of fruits and vegetables from a supermarket.

8 When is the GFF Study recruiting participants?

Recruitment for the GFF Study begins in June 2023 and will continue until 20 participants have been enrolled.

9 How long will the study last and how much time will it take?

The dietary trial component of the GFF Study will take 24 days and is planned to occur between August 1 and September 30, 2023. The actual dates of each participant’s dietary trial will depend on garden harvest times and personal scheduling. Participants are expected to spend an average of 20–30 minutes each day during the study collecting stool and produce samples and filling out the Daily Fruit & Vegetable Log.

10 Who makes sure this study is safe?

Review and oversight is conducted by the University of Oregon IRB (Institutional Review Board) continues throughout the study as investigators analyze survey and biological data. The IRB is a research oversight committee charged with assuring, both in advance and by annual review, that appropriate steps are taken to protect the rights and welfare of humans participating as subjects in approved research studies.

11 Will there be any ill effects on my health from participating in this study?

In this study you will be asked to eat fruits and vegetables harvested from your own garden, as well as from a supermarket. We do not expect any ill health effects from this protocol. However, we are unable to provide medical advice and you should ask your healthcare provider about personal health risks that could arise from participation. Your participation is voluntary and you can withdraw from the study at any time.

For GFF Study Participants

12 Can I choose when I start the dietary trial?

Yes, once you are enrolled as an active participant in the study, you may schedule the start date of your dietary trial for a time that is most convenient to you. An important consideration is the timing of your garden’s harvest bounty.

13 How will I know which part of the dietary trial I’m in?

Each day during the dietary trial you will fill out the Daily Fruit & Vegetable Log through Qualtrics, which should take less than 5 minutes. The first few questions will help you identify which part of the dietary trial you are in and what your responsibilities are for that day.

14 Can I take prescribed medications or supplements during the dietary trial?

Medications and supplements can be taken, however, use of any medications that would have been cause for exclusion (see Question 5) will require the participant to withdraw from the study.

15 What else can I eat or drink during the diet intervention periods?

As long as you are consuming the USDA-recommended amounts of fruits and vegetables for your BMI-adjusted caloric intake each day during the intervention periods, you can eat/drink as usual for the remainder.

16 I typically eat more than the USDA-recommended amounts of fruits and vegetables. Should I get them all from the same source or can I eat the USDA-recommended amount from one source and then get the remainder from a different source?

Ideally, you should get all your fruits and vegetables from your garden during one of the intervention periods and all from the supermarket during the other period. This would maximize our chance of seeing if there is a substantial difference in microorganisms between garden-fresh and store-bought produce.

17 I ran out of store-bought veggies for the week. Can I supplement with veggies from my garden?

Refer to previous answer.

18 Does a CSA box count as garden veggies or store bought veggies?

Unfortunately, it counts as neither. For this pilot study you must get your produce either from your garden or from a supermarket. Refer to question 4 for a more detailed explanation.

19 What should I do if I can’t eat the USDA-recommended amounts of fruits and vegetables one or more days?

If you are unable to meet the fruit/vegetable intake goal on one or more days during the study, please email Dr. Mhuireach ( for guidance.

20 What happens if I forget to record my fruit and vegetable consumption during the dietary trial? Can I enter the information at a later date?

If you forget to log your fruit and vegetable intake on one or more days during the dietary trial, you can enter the data through the Qualtrics survey as soon as you remember.

21 How do I collect stool samples?

You will collect your stool (fecal) samples using OmniGene Gut collection kits provided by the research team. The kits come with detailed printed instructions and you can also watch a short tutorial video here. Upon finishing each stool sample collection, affix the appropriate barcode label to the collection tube.

22 If I have more than one bowel movement per day, when should I collect the stool sample?

Collect the first full bowel movement of the day. Ideally, you will scoop small portions from several different locations of the stool, as there may be variability from the beginning to the end.

23 Do I have to store the stool samples in my home refrigerator/freezer?

No. The OmniGene Gut collection kits stabilize microbial DNA so that they can be stored at room temperature for up to 60 days.

24 How will I return all of the samples to the research team?

The research team will pick up your samples and transport them back to the laboratory. We will coordinate with you to schedule a pick-up time and location after you have completed both dietary intervention periods.

25 What will I learn about the microbiomes of my gut and my garden veggies?

It may take up to a year before all microbial sequencing and data analyses are complete. The research results that come from this study based on your samples will also be complex and difficult to interpret. Furthermore, they may not be definitive and should not be used to make medical decisions. For these reasons, results will be available only upon request.

Data Security and Privacy

28 Will my data be kept secure and confidential? How will this be done?

Utmost effort is made to protect the identity of the participants in this study. All information is kept secure and confidential with access only to the investigator who undergoes regular biomedical research ethics training. When your data are collected, they are labeled with a unique Participant ID rather than personal information, such as your name. All study materials are stored in a locked facility and secured computer files; your personal information is kept in separate files accessible only to the investigator. Your personal contact information will not be shared with anyone, although the IRB could have access to the data and personal identifiers.

29 How long will my samples and personal information be kept?

Your physical samples and personal information will be stored for the duration of the study and data analyses, but in no event longer than three years. Microbial sequencing data with no connection to your personal information will be stored indefinitely in the National Center for Biotechnology Information (NCBI) online repository.

If you have any other questions, please contact Dr. Mhuireach at