The probability of detecting Escherichia coli varies between host species with different diets and body sizes. An experimental study that mimicked the effect of different carnivore body masses found that digesta transit times influence E.coli abundance. In this study, we investigated how the host's gastrointestinal dynamics affected E.coli abundance and genotype in a system that reflected an herbivorous host. Forty rats from nine litters were fed a diet high in fermentable fibre. We found a small effect of fibre concentration on the difference between the liquid and particle digesta retention times. However, the rats' litter membership explained the majority of the retention time differences (79%). In turn, we found that as the difference between liquid and particle retention times increased, E.coli faecal cell densities decreased, while the likelihood that an animal's dominant E.coli strain possessed a gene involved in adhesion (agn43) increased. Thus, this experiment revealed an unanticipated high degree of association between the hosts' litter, their gastrointestinal dynamics and the E.coli genotypes. Furthermore, by comparing our findings to previous work, we show that the presence of fermentable fibre in the diet appears to change the relationship between the host's phenotype and E.coli.