Comparative transcriptome and gut microbiota analysis of Exopalaemon carinicauda with different growth rates from a full-sib family

In the breeding process of Exopalaemon carinicauda from the same family, noticeable differences often occur in growth characteristics under the same conditions. To investigate this issue, we performed a comparative transcriptome analysis to identify the critical genes involved in weight gain and compared the intestinal flora to screen for potential intestinal probiotics. In total, we identified 1311 differentially expressed genes (DEGs), of which 735 genes, including troponin C, chitinase, cathepsin B, cathepsin L, and trypsin, were upregulated exclusively in the fast growth group. Several DEGs were validated by quantitative real-time PCR and assigned to the ribosome, phagosome, apoptosis, purine metabolism, and Hippo signaling pathways. The microbiome community richness and diversity of the fast-growing individuals (FGIs) were higher than those of the slow-growing individuals (SGIs). In the current study, the intestinal microflora was mainly distributed in the Proteobacteria, Firmicutes, and Bacteroidota. The species with significant differences ( P  < 0.05) between the FGI and SGI groups included the iron-reducing bacteria, Nitrospira moscoviensis, Sulfuritalea hydrogenivorans, and Alpha proteobacterium. Our results provided insights towards revealing the mechanism underlying the growth differences in E. carinicauda.