Effects of Dietary Protein and Starch Digestion Rates on Jejunal and Cecal Microbial Community States and Feed Efficiency in Raccoon Dogs

Feed efficiency remains a significant challenge in farmed raccoon dogs, and performance differences can occur even when diets are formulated with similar nutrient levels. Beyond nutrient concentrations, digestion kinetics can alter the timing of carbon and nitrogen availability along the gastrointestinal tract, thereby influencing microbial assembly in a segment-specific way. Twenty 2-month-old male raccoon dogs (Nyctereutes procyonoides) were divided into four dietary groups (n = 5) in a 2 × 2 factorial design. The design combined protein-source formulations containing either soybean cake or dried distillers grains with solubles and starch-source formulations based primarily on either extruded corn or high-amylose corn starch, representing relatively rapid and slow expected digestion characteristics, respectively. The purpose was to assess how digestion-rate synchronization affects jejunal and cecal microbiota structure and whether community state types (CSTs) link diet and feed efficiency. Growth performance varied modestly among treatments, with group B showing the lowest feed-to-gain ratio (F/G) and highest average daily gain (ADG). Starch source significantly affected ADG, while protein and protein × starch interaction influenced F/G. Microbiota profiles were strongly segment-dependent: the cecum had higher richness and diversity than the jejunum. Two-way analyses and Bray–Curtis ordinations showed that the jejunal community was primarily associated with the protein × starch interaction, whereas the cecal community was associated mainly with the protein-source factor and the protein × starch interaction. Network analysis revealed more complex and densely connected microbial communities in the cecum, with core genera occupying central positions. Dirichlet multinomial mixture modeling, performed independently for each intestinal segment, identified two jejunal community states (J-CST1 and J-CST2) and two cecal community states (C-CST1 and C-CST2). J-CST1 and J-CST2 represented alternative lactic acid bacteria-dominated configurations, with J-CST2 enriched in Lactobacillus and J-CST1 characterized by higher abundances of Streptococcus and Bacillus. C-CST2 was represented predominantly by samples from group B and was characterized by higher abundances of Segatella and taxa affiliated with Bacteroidota and Lachnospiraceae. Predicted functional profiles differed between CSTs, involving pathways related to carbohydrate, amino acid, lipid, and bile acid metabolism. Mediation analysis did not provide consistent evidence of significant indirect effects for J-CST membership, whereas C-CST membership was associated with significant estimated indirect effects on final body weight, ADG, and F/G. These findings suggest that dietary protein- and starch-source combinations with different expected digestion characteristics drive segment-specific microbial patterns. Supported by taxonomic, network and functional evidence, cecal CSTs act as an intermediate ecological phenotype that partially explains the variation in growth efficiency, highlighting hindgut community states as potential targets for personalized nutrition of raccoon dogs.