Location: Diet, Genomics and Immunology Laboratory
2025 Annual Report
Objectives
1: Develop a refined New Total Western Diet for rodent studies and determine the effect of diet composition on gut microbiota composition, function, and experimental colitis. [NP107, C3, PS3B]
2: Determine the effect of different types and sources of resistant starches added to the modified New Total Western Diet on gut microbiota composition, function, and experimental colitis. [NP107, C3, PS3A, PS3B]
3: Determine the effect of different foods (cooked beans or fruits and vegetables) added to a Western style diet on gut microbiota composition, gastrointestinal function, and experimental colitis. [NP107, C3, PS3A, PS3B; C4, PS4A]
Subobjective 3A - Determine the impact of cooked beans on gut microbiome composition, function, and response to experimental colitis models in mice and swine.
Subobjective 3B: Determine the impact of fruit and/or vegetable supplemented diets at DGA recommended levels on gut microbiome composition and function in WD-Ossabaw pig model.
Subobjective 3C. Determine the effect of fruit and vegetable dietary supplementation on host inflammatory response against Dextran Sodium Sulfate (DSS) induced colitis in a WD Ossabaw pig model.
Approach
The studies proposed in the current project plan will use a complementary approach to take advantage of the strengths of each model system. Mice will be used as a lower-cost, high-throughput screening tool to evaluate the effect of RS and beans on the microbiome, metabolome, gene expression, and resistance to colitis. The proposed mouse models in this project plan will provide flexibility to evaluate several classes of dietary RS and beans at various concentrations and combinations to evaluate mucosal responses to both DSS- and bacterial- induced colitis. The results from these studies will be evaluated, and the most promising candidate foods will then be used to test mechanism-based effects in a pig model that is likely to yield data highly relevant to humans. Preliminary studies from our laboratory indicate that consumption of FVs improves the outcome of DSS-induced colitis in pigs, and this line of research will be explored further. The effects of RS, FVs, and beans on the pig microbiome, metabolome and glycome will be evaluated and correlated with changes to mucosal immunity. Data derived from this proposal will identify and characterize the host response after consumption of experimental diets targeted to be protective against inflammatory conditions. Results from the pig studies will inform recommendations for dietary RS, FV, and beans predictive of improved intestinal health in humans and can identify points of inquiry suitable for human trials.
Progress Report
In support of Objective 1, the rodent experiment diet is being humanized to better reflect human dietary patterns. Previous nutritional studies used a new Total Western Diet (TWD) (J Agric Food Chem. 2012 Jul 11;60(27):6736-42. doi: 10.1021/jf204509a) as a basal rodent diet, whose micro- and macro-nutrient composition was based on National Health and Nutrition Examination Survey (NHANES) data. While the TWD better approximated what was consumed by Americans, it had only one source of protein, casein, fiber, and cellulose. The TWD was modified based on NHANES food consumption data to contain multiple sources of protein, including eggs, casein, whey, wheat protein, chicken, beef (TWD-P); fiber, including wheat fiber, pectin, carrot fiber, and cellulose (TWD-F); or multiple sources of both protein and fiber (TWD-FP). The effect of feeding mice the AIN-93G diet was then compared; it is commonly used as a basal diet for nutritional studies that do not replicate the micro- and macro-nutrient content of an American diet to the original TWD and the three modified versions, TWD-F, TWD-P, and TWD-FP. Multiple tissues, including the cecum, colon, and liver, were collected along with fecal pellets and cecal contents for 16S, metagenomic, and meta-transcriptomic analysis as well as RNA sequencing for gene expression analysis of tissues.
In support of Objective 3, the existing Duroc genome was improved by monitoring and revising the assembly, annotation, and analysis of the porcine genome. For the Ossabaw genome, location data from the genome was added to the database, and 500 loci were checked for accuracy. The error rate found was similar to the other two Ensembl-curated genomes, indicating a need for manual annotation.
In support of Sub-objective 3C, the impact of feeding fruits and/or vegetables as a dietary supplementation using a Westernized diet was evaluated using a translational pig model. Twenty-four eight-week-old Ossabaw pigs were fed a westernized diet alone or supplemented with lyophilized veggies (V) including spinach, kale, green beans, celery, and broccoli; fruits (F), including strawberries, blueberries, blackberries, red apple, and seedless green grapes or a combination of these fruits and vegetables (FV) equivalent to a daily intake of 2.5 cups of fruit or 3.5 cups of vegetables as recommended for humans by the Dietary Guidelines for Americans (DGA). Clinical samples were collected throughout the seven-week dietary intervention to assess the longitudinal dietary changes on the host blood cell transcriptome and the gut microbiome. A cross-sectional sampling of biofluids (blood, urine, bile, intestinal contents) and tissues (intestine, lymph nodes, liver, brain, visceral fat) was done at the end of the intervention to compare the modulatory effects of F or V and FV supplemented diets on the host transcriptome, metabolome response to a westernized pro-inflammatory diet. All diets were isocaloric and adjusted for similar fiber contributions.
Accomplishments
1. Type 4 resistant starch derived from potato starch modulates the response to intestinal infection. Consumption of resistant starch can alter the host microbiome and bacterial fermentation, changes that have been linked to health benefits, but the effect of a specific type of resistant starch remains unclear. ARS scientist in Beltsville, Maryland, examined the effects of type 4 resistant starch using a rodent model of infection. It was observed that a commercially used type 4 resistant starch derived from potato can increase colonization and colon pathology induced by Citrobacter rodentium in a colitis mouse model and is related to the gut microbiome changes. The study provides critical science-based information on how specific types of resistant starch can impact host dietary response, and the need for a judicious choice of resistant starch in food product development to avoid deleterious health effects. Basic, translational, and health scientists in the field of food science, nutrition, and medicine will benefit from this information.
2. Westernized and heart-healthy diets differentially affect the brain micro vessel transcriptome. Diet is considered a modifiable neurodegenerative disease risk factor, but the mechanisms remain unclear. ARS scientists in Beltsville, Maryland, and researchers at Tufts University in Boston, Massachusetts, compared the effects of feeding a Westernized diet (WD) high in refined carbohydrates, cholesterol, and saturated fat relative to a heart-healthy diet (HHD) high in unrefined carbohydrates, polyunsaturated fat and fiber and low in cholesterol on brain micro vessel transcriptome and metabolome of the temporal region of the brain using the Ossabaw pig model. Pathways related to inflammation, angiogenesis, and apoptosis were enriched in the WD group, while cell energetics, neurotransmission, and inflammation resolution were enriched in the HHD group, with a differential profile in brain amino acids. These results provide evidence for the critical role of diet in brain micro-vessel gene expression and brain metabolome. The study provides science-based information to further elucidate molecular mechanisms in the brain that are regulated by diet and allow for the design of targeted dietary preventive approaches for reducing neurodegenerative disease risk.
Review Publications
Pletsch, E.A., Dawson, H.D., Cheung, L., Ragonese, J.S., Chen, C.T., Smith, A.D. 2025. A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a Western diet based on NHANES data. Food and Function. 16(9):3439-3464. https://doi.org/10.1039/d4fo04697h.
Solano Aguilar, G., Matuszek, G.H., Matthan, N., Lichtenstein, A.H., Wang, X., Lakshman, S., Barger, K., Bennett, R., Hyman, B.T., Lamon-Fava, S. 2024. Differential regulation of brain blood vessel transcriptome and brain metabolome by Western and heart-healthy diets in Ossabaw pigs. Scientific Reports. https://doi.org/10.1038/s41598-024-81321-1.