Effects of Different Feed Types on Intestinal Microbial Community Diversity and Intestinal Development of Newborn Siamese Crocodiles

Conventional alligator farming, characterized by reliance on chilled fish meat, faces significant challenges, including risks of bacterial contamination and nutritional imbalances. These issues heighten increasing disease susceptibility and threaten industry sustainability, underscoring the critical need for developing nutrient-dense, low-pathogenicity compound feeds. This study conducted a comparative analysis of newborn Siamese crocodiles fed either chilled fish meat or compound feed formulation. Intestinal microbial samples from both cohorts underwent 16S rRNA gene high-throughput sequencing to evaluate differences in microbial composition, diversity, and predicted functionality. The compound feed, specifically formulated for this investigation, possessed the following nutritional composition: crude protein 52.42%; digestible crude protein/digestible energy 16 mg/kcal; crude fat 12.31%; ash 17.42%; crude fiber 0.45%; starch 7.69%; digestible energy 3450 kcal/kg; lysine 3.66%; threonine 1.92%; methionine 1.27%; arginine 3.07%; total essential amino acids 22.97%; calcium 2.51%; total phosphorus 1.8%; available phosphorus 0.98%. Bioinformatics analysis revealed that the compound feed group exhibited numerically higher richness and alpha diversity indices within the intestinal microbiota compared to the chilled fish group. The microbial communities in both groups were dominated by the phyla Proteobacteria, Bacteroidetes, Fusobacteriota, and Firmicutes, collectively representing over 50% of the relative abundance. Functional prediction indicated that the compound feed group possessed the highest relative abundance in metabolic pathways associated with cofactor and vitamin metabolism, carbohydrate metabolism, amino acid metabolism, terpenoid and polyketide metabolism, lipid metabolism, and replication and repair. In contrast, the chilled fish group exhibited significant functional alterations in glycan biosynthesis and metabolism, translation, nucleotide metabolism, transcription, and biosynthesis of other secondary metabolites. Histomorphological analysis demonstrated greater villus height and crypt depth in the compound diet group compared to chilled fish group, although no significant differences were observed in crypt depth or the villus-to-crypt depth ratio. Collectively, these findings indicate that the compound feed enhances intestinal microbial diversity and optimizes its functional structure. Furthermore, while no statistically significant difference in small intestinal villus height was detected, the results suggest a potential positive influence on intestinal development. This investigation provides a scientific foundation for compound feed development, supporting sustainable breeding practices for Siamese crocodiles.