Growth-Associated Ecological Reorganization of the Gut Microbiota in Larimichthys crocea: Shifts in Microbial Persistence and Niche Breadth

Gut microbial communities undergo continuous reorganization during fish development, but changes in microbial persistence and ecological niche strategies across post-juvenile growth remain insufficiently understood. Here, we characterized the gut bacterial communities of cultured Larimichthys crocea across three successive body-size classes: EGC (5–8 g), MGC (39–46 g), and LGC (160–162 g). The three stages were successively sampled from the same cultured population maintained in the same culture pond. At each stage, 15 fish were sampled, and intestinal samples from three individuals were pooled to generate one pooled intestinal sample, yielding five pooled samples per stage. Fish received the same feed formulation throughout cultivation, while feeding quantity was adjusted according to growth. Rarefaction analysis indicated adequate sequencing coverage, and ASV-level community structure differed significantly among growth stages (ANOSIM, R = 0.4698, p = 0.001). Pseudomonadota remained the dominant phylum throughout growth, whereas pronounced restructuring emerged at finer taxonomic resolutions. EGC communities showed a comparatively consistent composition dominated by Methylobacterium, while MGC and particularly LGC exhibited substantial redistribution among dominant bacterial lineages. Stage-specific membership also changed with growth: unique genera increased from 36 in EGC to 48 in MGC and 50 in LGC, whereas stage-specific ASVs showed a nonlinear pattern and peaked in MGC (118, 173, and 124 unique ASVs in EGC, MGC, and LGC, respectively); 88 ASVs were shared across all three stages. Persistent taxa remained numerically important, accounting for 36.34%, 31.59%, and 36.95% of detected taxa in EGC, MGC, and LGC, respectively, but their contribution to total community abundance declined from 90.30% to 75.29% and 68.06%. Conversely, intermittent taxa increased in abundance contribution from 6.80% to 14.85% and 29.17%. Niche-breadth analysis further showed that specialists represented 74.38% of classified taxa and generalists 19.26%. Although generalists remained quantitatively dominant, their contribution declined from EGC to LGC, whereas specialist contribution increased. Growth-associated taxa further showed contrasting trajectories, particularly a progressive decline in Methylobacterium and increase in Aquabacterium. Collectively, these findings reveal pronounced ecological reorganization of the gut microbiota across successive size- and age-associated sampling stages of L. crocea. Because body size and age covaried with chronological sampling time in a single culture pond, these patterns should be interpreted as growth-associated temporal restructuring rather than as effects attributable solely to host growth.