Microbiome of different intestinal locations of Litopenaeus vannamei

Litopenaeus vannamei represents the most cultivated crustacean species, accounting for approximately 80% of global shrimp aquaculture output. The intestinal microbiota structure and functionality are known to critically influence L. vannamei growth. While previous investigations of shrimp gut microbes emphasized the whole intestine, limited research has examined the composition and functional differences of microbiota across specific intestinal sections in L. vannamei. In this study, healthy shrimp samples were collected and divided into four sections after removing the contents: S(stomach), H (from posterior stomach to the distal end of the hepatopancreas.), G (the section from hepatopancreass end to the sixth abdominal segment), and R(rectum). The microbial composition and function were analyzed across locations via 16S rRNA high-throughput sequencing. The results revealed that significant - and -diversity distinctions existed between sections (p<0.05). Microbial abundance and diversity were enriched within group G and H compared to group S and R. The result of PCoA analysis revealed similarities between group S, H, and G, while group R markedly differed (p<0.05). Three dominant phyla were identified across sections - Firmicutes (enriched in group S and H), Bacteroidota (enriched in group G) and Proteobacteria (enriched in group R). At genus level, Bacillus, Flavobacterium, Vibrio, and Mycoplasmataceae predominated (>10%) across sections. The rectum pathways including carbon, nitrogen, sulfur metabolisms were significantly elevated. Quorum sensing and two-component systems were also overrepresented in rectum. One-way network analysis showed that the dominant flora of group S, H and G were Bacillus, Mycoplasmataceae, and Flavobacterium, which are promoters of beneficial bacteria in the gut, while the dominant flora of rectumthe most competitive genus of bacteria in the intestinal tract was Vibrio,and Pseudofulvibacter, Alcaligenaceae, and Pseudomonas represent potential probiotic genera that could be screened as antagonists against Vibrio in the shrimp gut. In summary, we hypothesize the stomach and H sections degraded organic matter, G section absorbed and digested macronutrients, and rectum section recycled materials and participated in circular metabolism. These segment-specific analyses provide novel perspectives into section-specific microbial interactions and functions along L. vannamei intestine.