Functional Feed Additives Promote Recovery from Runting and Stunting Syndrome in Apostichopus japonicus: Links Between Growth Traits, Digestive Function, and the Gut Microbiome

Runting and stunting syndrome (RSS) has been reported worldwide in commercial aquaculture and is frequently observed in juvenile-rearing ponds of Apostichopus japonicus. The objective of this study was to use commercially cultured A. japonicus naturally affected by RSS under high-density culture conditions as the study subjects. Different nutritional additive treatments, including marine mud, effective microorganisms (EM; photosynthetic bacteria, lactic acid bacteria, yeasts, and actinomycetes), yeast, kelp powder, and fermented kelp powder, were applied, and growth performance during recovery, the activities of intestinal digestive enzymes (protease, alginate lyase and cellulase), and heterotrophic bacterial counts were systematically evaluated. The results showed that the recovery rate of RSS in A. japonicus decreased in the following order: the EM group (90.91 ± 1.15%), the fermented kelp group (90.91 ± 4.96%), the yeast group (81.82 ± 5.99%), the kelp group (72.73 ± 1.35%), the marine mud group (63.64 ± 1.41%), and the control group (54.55 ± 1.47%). Moreover, increased intestinal digestive enzyme activities, elevated heterotrophic bacterial counts, and a reduced relative abundance of Vibrio were identified as key factors associated with RSS recovery in A. japonicus, with the EM and fermented kelp groups showing the most pronounced effects. High-throughput sequencing further revealed that nutritional additive treatments differed in their effects on the intestinal microbial community structure of RSS-affected A. japonicus. At the phylum level, Bacillota (26.45–48.08%), Actinomycetota (13.96–44.99%), and Pseudomonadota (9.15–56.46%) were the dominant phyla in the intestine of A. japonicus. At the genus level, a lower relative abundance of Vibrio was associated with improved recovery, and groups with lower Vibrio levels generally exhibited better recovery outcomes; notably, the EM group showed the lowest relative abundance of Vibrio (1.37%). Overall, these community shifts may contribute to recovery by supporting potential energy supply, immune regulation, and functional restoration. Therefore, these findings provide new insights into the treatment of RSS in A. japonicus through the development of beneficial microbes and the targeted suppression of potential pathogens.