Diet-induced metabolic and faecal microbiome responses in pet dogs fed a minimally processed versus extruded kibble diet

Introduction The extent to which food is processed influences gut functions, such as digestion, nutrient uptake, and microbiome response, with the potential to impact immuno-metabolic health. Despite known associations between ultra-processed food (UPF) intake and chronic diseases in humans, mechanistic links explaining inferred health risks remain unclear. Health risks associated with chronic disease are also a concern for companion animals such as dogs, where nutritionally complete dry processed foods constitute a major component of contemporary pet dog diets. A challenge is that nutrition is complex and even diets based on nutritionally complete processed foods typically vary in multiple dimensions. Methods Here, we use a randomised, cross-over design to compare short-term effects of two commercially available nutritionally complete canine diets—an extruded kibble diet (EKD) and a mildly cooked, minimally processed diet (MPD). We assigned 24 healthy dogs to one of two groups: all dogs remained on their at-home diet for 1 week, before transitioning to (1) MPD or (2) EKD for 2 weeks each. One dog was removed from the study due to health complications, and the remaining 23 dogs completed both dietary treatment periods. Glycaemic, hormonal, and gut microbiome responses were captured from pre- and post-prandial blood samples and time series of 12 faecal samples from each dog. Results The experimental diets resulted in distinct physiological and gut microbiome responses. MPD was associated with improved faecal consistency (FCS 2.24 ± 0.67, p = 0.005), lower pre- and post-prandial gastric inhibitory polypeptide (GIP, p < 0.001) and peptide YY (PYY, p < 0.05), and reduced post-prandial glycaemic response compared to EKD (AUC, p = 0.009). Diet was the strongest predictor of microbial response despite between-dog differences, with higher alpha diversity associated with MPD and greater within-individual community turnover following transition to MPD in both treatment groups (Group 1, p < 0.001; Group 2, p < 0.05). Conclusion These data show the feasibility of testing diet formulations in pet dogs and understanding the role of host–microbiome interactions in responses to food. The demonstration of distinct outcomes highlights the need for further studies on long-term feeding to better understand mechanisms and implications for health in community pets.