Characterization of Gut and Gill Microbiomes in Fast-Growing Pacific White Shrimp Penaeus vannamei

The relationship between microbial communities and their hosts is important to the health and productivity of marine animals in aquaculture. This study investigated the microbiomes in the gut and gill of Penaeus vannamei using 16S rRNA gene sequencing, comparing the microbial characteristics in the fast-growing trait and in the control group. Fast-growing individuals exhibited significantly different growth parameters and gut/gill microbiomes. Significantly higher weight gain and condition factors, as well as lower hepatosomatic indices (HSI), were observed in fast-growing individuals. Fast-growing individuals also displayed significantly higher operational taxonomic unit (OTU) counts (in gills) and greater phylogenetic diversity (PD) in both gut and gill microbiomes, while Lactobacillus was significantly more abundant and showed strong network centrality in the gut of this group. Furthermore, beta diversity analysis revealed significant differences in microbial community structure between the groups in both gut and gills. Functional predictions indicated increased activity in metabolic pathways (e.g., carbon metabolism, protein export) in the fast-growing group, reflecting the adaptations to increased energy utilization. Conversely, other genera such as TM7a were found at significantly lower abundance in the fast-growing group and showed significant correlations with growth parameters, highlighting potential microbial indicators of different growth strategies or physiological trade-offs. These findings underscore the close relationship between microbial communities and the health and productivity of Penaeus vannamei. Future studies should focus on optimizing growth performance and balancing it with the immune robustness in P. vannamei.