Growth-Associated Gut Microbiota Succession in Decapterus maruadsi: Increasing Dominance of Persistent Taxa

Gut microbiome development during fish growth involves not only taxonomic turnover but also changes in the persistence and ecological dominance of microbial members. Here, we characterized the gut microbiota of D. maruadsi across three successive growth-associated body-size groups: the early-growth group (BLEGC; 4.98–6.81 g), middle-growth group (BLMG; 16.67–19.63 g), and late-growth group (BLLGC; 27.30–28.66 g). The three groups were successively sampled from the same cohort continuously reared in the same culture system. Fish received the same diet formulation throughout cultivation, with feeding quantity adjusted according to growth stage. At each stage, 15 fish were sampled, and rinsed intestinal tissues from five individuals were pooled to generate one composite sample, yielding three pooled intestinal samples per growth stage. Gut bacterial communities differed significantly among growth stages (ANOSIM: R = 0.2593, p = 0.005), while Pseudomonadota remained the dominant phylum across all groups. Complementary PERMANOVA supported an overall stage-associated difference, although PERMDISP also indicated heterogeneous multivariate dispersion among stages. Growth-associated restructuring became more evident at finer taxonomic levels and was accompanied by a pronounced contraction of stage-specific microbial membership. The number of unique ASVs declined from 361 in BLEGC to 286 in BLMG and 69 in BLLGC, whereas 84 ASVs were shared across all three stages. Forty ASVs met the global persistent criterion of detection in at least eight of the nine pooled samples, and their abundance contribution increased from 58.43 ± 15.08% in BLEGC to 79.54 ± 6.38% in BLMG and 90.14 ± 2.14% in BLLGC. When mean abundance was calculated only among samples in which each ASV was detected, prevalence remained positively associated with conditional mean abundance. Collectively, these results indicate that growth-associated gut microbiome succession in D. maruadsi involves not only taxonomic turnover but also progressive redistribution of community abundance toward highly prevalent and persistent bacterial members.