Effects of Intestinal Microbiota on Individual Growth and Development of Pontastacus leptodactylus

Pontastacus leptodactylus is an aquatic resource endemic to Xinjiang, and its growth performance is closely related to the composition and structure of its intestinal microbiota. This study used male P. leptodactylus, divided into a high-growth-performance (HGP) group and a low-growth-performance (LGP) group based on growth rates, to analyze differences in intestinal microbiota using microbial sequencing technology. Results showed that the number of ASVs unique to the HGP group (7840, accounting for 65.97%) was substantially higher than that in the LGP group (3383, 28.46%). ALDEx2 analysis identified six ASVs significantly enriched in the LGP group, assigned to Methylobacterium, Devosia, order Rhizobiales, Renibacterium, Stenotrophomonas, and class Mollicutes, which were near-absent in the HGP group. At the phylum level, TM7 was differentially abundant with higher relative abundance in HGP. At the genus level, ten genera showed significant differences: Pseudomonas, Hydrogenophaga, Mesorhizobium, Reyranella, Mycobacterium, Flavobacterium, Ralstonia, Bradyrhizobium, and Aeromicrobium were enriched in HGP, whereas the opportunistic pathogen Plesiomonas was depleted. Alpha diversity analysis revealed significantly higher Chao1, observed species, Shannon, and Faith’s pd indices in the HGP group (p < 0.05). Beta diversity analysis confirmed significant separation in microbial community structure between the two groups (adonis p = 0.018). KEGG pathway analysis showed upward trends in retinol metabolism, shigellosis, geraniol degradation, and xenobiotics metabolism pathways in HGP (p < 0.10), and a significant upregulation of coumarin biosynthesis (p < 0.01). COG analysis revealed eight downregulated functional genes in HGP (p < 0.01), suggesting more complex host–microbiota interactions. This study identifies distinct intestinal microbial signatures associated with growth performance in P. leptodactylus, providing candidate targets for probiotic development and aquaculture management, while causal verification remains the critical next step.