Research Project: Impact of Diet on Intestinal Microbiota, Gut Health and Immune Function

Location: Diet, Microbiome and Immunity Research

2022 Annual Report

Accomplishments
1. Antimicrobial resistance is lower with diverse, high-fiber diets. Antibiotic resistance is expected to be a major cause of death worldwide in the coming decades. ARS researchers in Davis, California, sought to understand how diet is related to the antimicrobial resistance of microbes in healthy adults. Bacterial DNA from fecal samples was examined in relation to the diet of healthy men and women who were normal weight, overweight, or moderately obese. The researchers found that the intestinal bacteria of individuals who consumed diverse diets that were high in fiber had lower levels of antibiotic resistance. than individuals with less diverse diets. These results suggest that dietary modification towards a more diverse, fiber-rich diet may reduce the individual and population-scale burden of bacterial infections resistant to antibiotics.

2. More diverse gut microbiomes co-occur with diverse sources of carbohydrates from food. A high-fiber diet has strong associations with better health, likely because of fermentation products produced by the bacteria in our colon on our own physiology. However, many types of fiber exist that interact uniquely with gut bacteria and current food databases do not adequately describe these various dietary fiber types. ARS researchers in Davis, California, addressed this limitation by assembling self-reported fiber-containing foods from 343 healthy U.S. adults into a tree structure describing their relatedness to capture the diversity of fiber types found in the diet. The variety of fiber-containing foods consumed was strongly associated with the diversity of the gut bacterial community. These results suggest that current dietary guidance that recommends higher fiber intake, but does not address fiber types, should also consider fiber diversity as an approach to improving health for Americans.

3. Machine learning identifies fecal pH as a predictor of bone health. Bone mineral content (BMC) and bone mineral density (BMD) are related to bone health and risk of osteoporosis. While it is known that certain factors, such as calcium intake, affect bone health, previous studies have been limited to analysis of variables of interest or to a specific subset of the population. ARS researchers in Davis, California, used machine learning models, which can find complex patterns in data, to predict BMC and BMD in a healthy men and women. Low stool pH, which is an indicator of more fermentation of dietary fiber in the colon, was predictive of higher BMC/BMD. This discovery suggests that dietary modifications that increase fermentable fiber and lower fecal pH, may also improve bone health in a general population.

Review Publications
Chin, E.L., Van Loan, M., Spearman, S., Bonnel, E.L., Laugero, K.D., Stephensen, C.B., Lemay, D.G. 2021. Machine learning identifies stool pH as predictor of bone mineral density in healthy multiethnic US adults. Journal of Nutrition. 151(11):3379-3390. https://doi.org/10.1093/jn/nxab266.
Dimitratos, S., Hercules, M., Stephensen, C.B., Cervantes, E., Laugero, K.D. 2021. Association between physiological stress load and diet quality patterns differs between male and female adults. Physiology and Behavior. 240. Article 113538. https://doi.org/10.1016/j.physbeh.2021.113538.
Artegoitia Etchev, V.M., Krishnan, S., Bonnel, E.L., Stephensen, C.B., Keim, N.L., Newman, J.W. 2021. Healthy eating index patterns in adults by sex and age predict cardiometabolic risk factors in a cross-sectional study. Biomed Central (BMC) Nutrition. 7. Article 30. https://doi.org/10.1186/s40795-021-00432-4.
Kable, M.E., Chin, E.L., Storms, D.H., Lemay, D.G., Stephensen, C.B. 2021. Tree-based analysis of dietary diversity captures associations between fiber intake and gut microbiota composition in a healthy U.S. adult cohort. Journal of Nutrition. 152(3):779-788. https://doi.org/10.1093/jn/nxab430.
James, K.L., Gertz, E.R., Cervantes, E., Bonnel, E., Stephensen, C.B., Kable, M.E., Bennett, B.J. 2022. Diet, fecal microbiome, and trimethylamine N-oxide in a cohort of metabolically healthy United States adults. Nutrients. 14(7). Article 1376. https://doi.org/10.3390/nu14071376.
Oliver, A., Xue, Z., Villanueva, Y.T., Durbin-Johnson, B., Alkan, Z., Taft, D.H., Liu, J., Korf, I., Laugero, K.D., Stephensen, C.B., Mills, D.A., Kable, M.E., Lemay, D.G. 2022. Association of diet and antimicrobial resistance in healthy U.S. adults. mBio. 13(3). Article e00101-22. https://doi.org/10.1128/mbio.00101-22.
Coates, L.C., Storms, D.H., Finley, J.W., Fukagawa, N.K., Lemay, D.G., Kalscheur, K., Kable, M.E. 2022. A low starch and high fiber diet intervention impacts the microbial community of raw bovine milk. Current Developments in Nutrition. 6(6). Article nzac086. https://doi.org/10.1093/cdn/nzac086.
Trott, J.F., Schennink, A., Horigan, K.C., Lemay, D.G., Cohen, J.R., Famula, T.R., Dragon, J.A., Hovey, R.C. 2021. Unique transcriptomic changes underlie hormonal interactions during mammary histomorphogenesis in female pigs. Endocrinology. 163(3). Article bqab256. https://doi.org/10.1210/endocr/bqab256.
Castillo, J.J., Couture, G., Bacalzo, N.P., Chen, Y., Chin, E.L., Blecksmith, S.E., Bouzid, Y.Y., Vainberg, Y., Masarweh, C., Zhou, Q., Smilowitz, J.T., German, J.B., Mills, D.A., Lemay, D.G., Lebrilla, C.B. 2022. The development of the Davis Food Glycopedia - A glycan encyclopedia of food. Nutrients. 14(8). Article 1639. https://doi.org/10.3390/nu14081639.
Tagkopoulos, I., Brown, S.F., Liu, X., Zhao, Q., Zohdi, T., Earles, J.M., Nitin, N., Runcie, D.E., Lemay, D.G., Smith, A.D., Ronald, P.C., Feng, H., Youtsey, G.D. 2022. Special report: AI Institute for next generation food systems (AIFS). Computers and Electronics in Agriculture. 196. Article 106819. https://doi.org/10.1016/j.compag.2022.106819.
Norris, S., Frongillo, E., Black, M., Dong, Y., Fall, C., Lampl, M., Liese, A., Naguib, M., Prentice, A., Rochat, T., Stephensen, C.B., Tinago, C.B., Ward, K., Wrottesley, S.V., Patton, G.C. 2021. Nutrition in adolescent growth and development. Lancet. 399(10320):172-184. https://doi.org/10.1016/S0140-6736(21)01590-7.
Newman, J.W., Krishnan, S., Borkowski, K., Adams, S.H., Stephensen, C.B., Keim, N.L. 2022. Assessing insulin sensitivity and postprandial triglyceridemic response phenotypes with a mixed macronutrient tolerance test. Frontiers in Nutrition. 9. Article 877696. https://doi.org/10.3389/fnut.2022.877696.