Unmelted, melted, and deconstructed Cheddar cheese: effects on the gut microbiome from a human dietary intervention study

Introduction Cheddar cheese is a nutritionally dense food matrix containing nutrients and bioactives with the potential to influence gut microbial characteristics. Food matrices influence nutrient absorption and digestibility, therefore the dairy matrix may affect gut microbial responses to dairy food intake. This research aims to identify gut microbial responses to Cheddar cheese consumption, considering aspects of the dairy matrix. Methods Secondary analysis was conducted on a subset ( n = 69) of participants’ data collected during a 6-week parallel 3-armed intervention study. Interventions involved daily consumption of one of the following: (A) 120 g unmelted Cheddar cheese; (B) 120 g melted Cheddar cheese; (C) butter (49 g), calcium caseinate powder (30 g), and Ca supplement (500 mg). Demographics, anthropometry, dietary intake and fecal samples were collected at baseline (V1) and post-intervention (V2). Fecal samples underwent 16S rRNA gene sequencing, followed by bioinformatic processing and statistical analysis. Results At V1, 52% were female, mean age was 58.2 ± 5.4 years, with no significant differences between groups or timepoints. Following sequencing, 12,098 unique bacterial taxa in total were identified. Under a False Discovery Rate (FDR) cutoff of 0.1, Dorea ( W = 0.568, FDR = 0.079) and Erysipelotrichaceae UCG-003 ( W = 0.887, FDR = 0.097) were significantly increased from V1 to V2 in the unmelted cheese group. At V2, Bacteroides was differentially more abundant in the unmelted cheese group, relative to the melted group ( W = 0.587, FDR = 0.034). Bacterial alpha diversity (Shannon, Simpson) significantly increased in the unmelted cheese group only from V1 to V2 ( p 0.05). Beta diversity analysis showed a significant group effect considering both timepoints ( F = 1.505, p 0.01). Considering V2 only, Principal Coordinate Analysis showed the unmelted group clustered more closely relative to the other groups, although the effect was not significant. Discussion Unmelted Cheddar cheese modulated the gut microbiome by increasing alpha diversity and abundance of several fermenting bacteria. Overall community structure also became more similar following consumption of unmelted cheese, relative to the other groups. Heating cheese and altering its physical structure disrupts the dairy matrix, potentially influencing downstream gut-nutrient interactions and subsequent gut microbial response.