Longitudinal Microbiome Investigations Reveal Core and Growth-Associated Bacteria During Early Life Stages of Scylla paramamosain

In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (<i>Scylla paramamosain</i>) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. In this study, we first characterized stage-specific microbiomes and shifts in the contributions of live feed and water via SourceTracker. We observed decreased microbial diversity and increased priority effects along zoea stages. <i>Psychobacter</i> was identified as the core genus, whereas <i>Lactobacillus</i> was the hub genus connecting different stages. Second, microbial correlations with various stage-specific growth traits were observed under interventions generating enhanced (probiotic mixture enrichment), normal (control), and reduced (antibiotic treatment) microbiomes. By combining machine learning regression and bioinformatics analysis, we identified four candidate growth performance-associated probiotics belonging to <i>Rhodobacterales</i>, <i>Sulfitobacter</i>, <i>Confluentimicrobium</i>, and <i>Lactobacillus</i>, respectively. Our study interpreted the dynamics and origins of the <i>Scylla paramamosain</i> zoea microbiome and underscored the importance of optimizing potential probiotics to increase growth performance during early life stages in marine invertebrates for effective larviculture.