Diet quality, gut microbiome, and inflammatory signatures in Puerto Rican adults with Crohn disease: a multidimensional analysis

Abstract Background and Aims Diet is increasingly recognized as a modifiable factor influencing gut microbiome and outcomes in Crohn disease (CD), yet data in underrepresented populations remain limited. We evaluated diet quality, dietary patterns, gut microbiome composition, inflammatory markers, and patient-reported outcomes in adults with CD from Puerto Rico. Methods We conducted a cross-sectional analysis of 60 adults with CD enrolled prior to dietary intervention in a parent study. Dietary intake was assessed using 24-hour recalls and evaluated using the Healthy Eating Index-2015 (HEI-2015), Alternative Healthy Eating Index-2010 (AHEI-2010), and exploratory dietary pattern analysis. The gut microbiome was assessed by shotgun metagenomic sequencing. Clinical outcomes included fecal calprotectin, C-reactive protein (CRP), a 96-cytokine panel, short Crohn Disease Activity Index (sCDAI), and short Inflammatory Bowel Disease Questionnaire (sIBDQ). Associations were evaluated using unadjusted and adjusted models with false discovery rate (FDR) correction. Results Overall diet quality was poor and characterized by low intake of fruits, vegetables, whole grains, and fiber, alongside high intake of saturated fat, added sugars, and animal-derived protein. Four dietary patterns were identified: vegetable-rich, dairy-rich, fruit-rich, and coffee/sweetener-rich. Participants adhering to the fruit-rich pattern exhibited the highest diet quality scores. Higher HEI-2015 scores were associated with greater gut microbial diversity and differences in overall microbiome composition. Participants with greater adherence to the vegetable-rich pattern showed modest increases in microbial diversity. Exploratory analyses suggested that higher fruit intake and adherence to a fruit-rich dietary pattern were associated with lower fecal calprotectin and CRP levels, whereas adherence to a vegetable-rich pattern was associated with better health-related quality of life (HRQoL) and adherence to a coffee/sweetener-rich pattern was associated with a worse symptom burden. However, no associations between dietary metrics and inflammatory markers, cytokines, or clinical outcomes remained significant after FDR correction. Most participants were in clinical remission despite substantial impairment in HRQoL. Conclusions Adults with CD in Puerto Rico exhibited poor diet quality that was associated with gut microbial diversity and exploratory differences in clinical outcomes. While these findings support the influence of diet on the microbiome and clinical outcomes, larger longitudinal studies are needed to determine whether dietary improvements can influence disease outcomes this underrepresented population.