Location: Diet, Genomics and Immunology Laboratory
2023 Annual Report
Objectives
Objective 1: Determine if polyphenol rich diets prevent microbiome dysbiosis, inappropriate activation of Toll and NOD-like receptor (TLR/NOD-like receptors) and reduce the severity of colitis in pigs. [NP107, C3, PS3B]
Objective 2: Compare consumption of polyphenol-rich foods combined with probiotics early in life for amelioration of systemic inflammation induced by a westernized high fat diet. [NP107, C3, PS3B, C4, PS4A]
Objective 3: Establish if consumption of polyphenol-rich foods will normalize westernized high fat diet-induced microbiome dysbiosis and prevent generalized inflammation. [NP107, C3, PS3B C4, PS4A]
Approach
The overall goal of the proposed research is to understand the complex interactions between diet, gut microbiome and host responses that are critical for the prevention of diseases associated with poor diet choices. The objective is to use a human-relevant pig model to understand mechanisms of intestinal dysregulation during consumption of a westernized-diet, which is strongly associated with obesity and related metabolic diseases, and to evaluate the incorporation of dietary probiotics, fruits and vegetables as an approach to attenuate the adverse consequences of consuming a westernized-diet. To achieve this goal, we propose to study the time-dependent changes in broad host health biomarkers within the immunome, microbiome and metabolome, and the dietary interventions that modulate these biomarkers. Our central hypothesis is that a modified westernized dietary pattern that contains recommended levels of fruits and vegetables will promote a healthier host microbiome due a polyphenol-induced prebiotic effect and anti-inflammatory responses.
Progress Report
Continued progress has been made for integration of -omics data derived from pigs fed a fruit and vegetable (FV)-supplemented diet and later exposed to a Dextran sodium sulfate (DSS) treatment to induce colitis. Completed Shotgun metagenomic sequencing from proximal colon contents, longitudinal fecal microbiota taxonomy data from five datapoints and localized transcriptome changes in intestinal mucosa and blood will be integrated to identify potential association of dietary FV levels with responsive host clinical biomarkers. Several bioinformatic approaches are being tested and compared for multi-omics integration of metagenome/transcriptome data, visualization and identification of diet-induced features associated with resistance to colitis. Manuscript is under preparation.
In collaboration with the Methods and Application of Food Composition Lab (MAFCL) scientists, mass spectrometry-analysis of longitudinal fecal samples collected after FV-supplementation and DSS challenge has been done to identify low intensity dietary FV-derived metabolites. Over 40,000 ion features from raw data are currently being analyzed for their relationship with diet-induced changes in bacterial taxonomy. A time and FV-dose dependent increase as early as one-week post-intervention has been detected in the full FV-dose treatment group for catechin and protocatechuic acid, two metabolites associated with fruit consumption and known for their antioxidant effects by scavenging reactive oxygen species. Similarly, a gut bacteria-based metabolite (5,3',4'-Trihydroxy-3-methoxy-6,7-methylenedioxyflavone) reported to be derived only from spinach was also detected in a time and dose-dependent manner. Metabolome abundance in urine samples is currently being analyzed for their relationship with synchronous metagenome data collected from proximal colon contents. The proposed statistical approach will be to identify bacterium, metabolite pairs that exhibit changing relationships in response to DSS alone or in combination with two different levels of FV supplementation.
In collaboration with the Nutritional and Clinical Glycomics Laboratory at the Department of Biochemistry and Molecular Medicine, School of Medicine at UC Davis, monosaccharide composition analysis of FV-diets has been completed. Progress has been done with characterization of longitudinal plasma samples collected from FV-DSS colitis experiment. Plasma samples were analyzed on the Nano-LC chip-TOF using an in-house N-glycan developed method. Preliminary data comparing the full FV treated group against baseline level indicated an increase in syalylated and fucosylated structures and reduced high mannose, sialofucosylated and undecorated glycan structures. Relationship of glycosylation with resistance to colitis will be analyzed across different dietary treatment groups.
The impact of Fruit and vegetable (FV) and/or probiotic (pb) supplementation of a Westernized diet on host metagenome and transcriptome response was evaluated. Four diets (Control, FV, pro and FV-pro) were fed to conventional grower pigs for seven weeks. Metagenome analysis of proximal colon contents indicated significant difference in alpha diversity according to diet (p<0.05) not probiotic with no effect on functional profiles. Differential gene expression analysis from intestinal mucosa is being done.
In collaboration with Human Nutrition Research Center on Aging (HNRCA), we studied the effects of diet on brain blood vessels in the Ossabaw minipig. Thirty-two pigs were fed an isocaloric Western diet (WD) or heart-healthy diet (HHD), with or without statin (S, atorvastatin). Neurovascular units were isolated from the brain temporal region and subjected to transcriptomic analysis. Metabolomic profiles of the temporal region were also evaluated. Differential gene expression and metabolite profile in WD-fed pigs relative to HHD suggest a likely contribution of diet to brain pathologies characterized by neuroinflammation and neurodegeneration. Manuscript is being prepared.
Accomplishments
1. Probiotic supplementation alters host tissue metabolite composition. Prolonged ingestion of a higher-fat diet, one cause of obesity, results in alterations to the gut microbiome. These alterations are implicated to have a profound role in the evolution and progression of obesity-linked diseases. Probiotics are associated with positive health effects such as limiting pathogen colonization, aiding in digestion, and vitamin synthesis. Using Ossabaw pigs as a model for obesity, and in conjunction with our previous research, ARS scientists in Beltsville, Maryland, performed an in-depth, nontargeted, metabolomic analysis on select organs to elucidate the effects of dietary supplementation with the probiotic Lacticaseibacillus paracasei. We focused our analysis on the effects of probiotic supplementation on a higher-fat (obesogenic) diet and a nutritionally balanced diet. Notably, our findings reveal that the brain cortex is highly sensitive to dietary influencers. After probiotic supplementation, several aberrant metabolites associated with a higher-fat diet revert to healthy levels, thus demonstrating the potential for a probiotic intervention for obesity-linked disease.
