About the GFF Study

garden salad on a shovel

Did you know that every day, we eat billions of microbes (bacteria, fungi, viruses) inhabiting our food? 

For example, Wassermann et al. (2019) estimated that a single apple harbors about 100,000,000 bacteria alone. Although food processors and manufacturers are careful to test for known pathogens, those comprise only a minuscule percentage of all the microbial life out there. And, since food testing is typically performed in the processing plant, not at the dinner table, we don’t really know which microbes live on and in the different types of food at the time we are eating them.

I am especially interested in microbes inhabiting fruits and vegetables harvested from backyard and community gardens. I speculate that garden-fresh foods have been subjected to less washing and sanitizing than supermarket produce and, thus, may still harbor indigenous plant- and soil- associated microbiota at the point of consumption. A recent study by Brown et al. (2022) found that during peak harvesting season, families that garden regularly and consume a substantial portion of their diet directly from their gardens tended to have more soil-associated bacteria in their feces than non-gardening families. Rather than being cause for alarm, these exposures are thought to be generally benevolent with regard to human health. For the vast majority of human evolution, exposure to soil- and plant-associated microbiota has been unavoidable and, in fact, may be important for maintaining health (Rook 2021). Supporting this theory, emerging evidence suggests that exposure to diverse microorganisms, such as those associated with traditional farm environments, can help train the immune system and reduce inflammation (Stein et al. 2016). In comparison, supermarket produce undergoes extensive handling and processing throughout its lengthy supply chain, and each instance of handling by human workers or contact with processing surfaces and liquids may alter the intrinsic microbiome of fresh fruits and vegetables. Dramatic changes in microbial composition from harvest to point of sale have been documented for supermarket produce. In some cases, fewer than 2% of the original microbial taxa remained at the point of sale; however, this was not a reduction in overall abundance of microbes but rather a shift from indigenous communities to other microbes acquired from the processing environment.

To better understand differences between the microbial communities of garden-fresh and store-bought fruits and vegetables, as well as their potential to influence the human gut microbiome, I am conducting a USDA-funded pilot study engaging 20 volunteers in a diet intervention. If you choose to participate, you will be asked to undergo two week-long diet intervention periods during which you will eat the USDA-recommended amount of fruits and vegetables. In one period all of the produce should be sourced from your garden and in the other the same produce should be sourced from a supermarket. You will be also asked to pre-plan your meals for the intervention periods, complete a Lifestyle, Health, & Diet Questionnaire, maintain a Daily Fruit & Vegetable Log, collect samples of all the fruits and vegetables you eat, collect stool (fecal) samples, and collect a tapwater sample. The total duration of participation is 24 days, with an expected average time commitment of 20–30 minutes per day. If you are interested in learning more, check out the FAQ or go directly to the screening survey to see if you are eligible.


Brown, M. D., Shinn, L. M., Reeser, G., Browning, M., Schwingel, A., Khan, N. A., & Holscher, H. D. (2022). Fecal and soil microbiota composition of gardening and non-gardening families. Scientific Reports12(1), 1595. https://doi.org/10.1038/s41598-022-05387-5

Rook, G. A. W. (2021). Darwinian Medicine: We Evolved to Require Continuing Contact with the Microbiota of the Natural Environment. Evolution Turns the Inevitable into a Necessity. In C. J. Hurst (Ed.), Microbes: The Foundation Stone of the Biosphere (pp. 327–364). Springer International Publishing. https://doi.org/10.1007/978-3-030-63512-1_18

Stein, M. M., Hrusch, C. L., Gozdz, J., Igartua, C., Pivniouk, V., Murray, S. E., Ledford, J. G., Marques dos Santos, M., Anderson, R. L., Metwali, N., Neilson, J. W., Maier, R. M., Gilbert, J. A., Holbreich, M., Thorne, P. S., Martinez, F. D., von Mutius, E., Vercelli, D., Ober, C., & Sperling, A. I. (2016). Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. New England Journal of Medicine375(5), 411–421. https://doi.org/10.1056/NEJMoa1508749

Wassermann, B., Müller, H., & Berg, G. (2019). An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? Frontiers in Microbiology10, 1629. https://doi.org/10.3389/fmicb.2019.01629