Bacterial populations were characterised during the in vitro fermentation of three standard polyphenols: ferulic acid, (+/-)-catechin and cyanidin-3-glucoside, adsorbed individually or in combination to apple cell walls (ACW). During fermentation with porcine faeces, samples were collected at regular time-points (up to 72 hours) for bacterial 16S rRNA gene sequencing. Significant differences in microbial populations (classified taxa) were noted between polyphenolic groups tested (P<0.0001). Principal taxa identified to be associated with substrate groups were: Parabacteroides with cyanidin-3-glucoside, Phascolarctobacterium with ferulic acid and the Clostridiales order with (+/-)-catechin. The presence of cyanidin-3-glucoside resulted in the most significant differences between bacterial communities during fermentation of the ACW substrate. The cyanidin-3-glucoside adsorbed to ACW, behaved similarly to the combination triple polyphenolic treatments. This study has demonstrated the use of a simplified model to indicate any microbial effects of polyphenols associated with dietary fibre in whole fruits. This work has shown that individual polyphenols, or adsorbed to PCW, have potentially very different effects on the gut bacteria.