Host Genome Drives the Diversity, Richness, and Beneficial Microbes in the Shrimp Microbiota: A Hologenome Perspective

Despite the growing understanding of the factors influencing the shrimp microbiome, the impact of host genetics on modulating the intestinal microbiota still needs to be studied. Moreover, the existing studies were typically conducted using animal models and under laboratory conditions. Here, we investigated the effect of two shrimp genetics, fast-growth (Gen1) and disease-resistant (Gen2), on shaping the microbiota of the hepatopancreas and the intestine in open-pond aquaculture farming conditions. First, we identified significant genomic differences between the two genetic lines using genome-wide SNP analysis. Then, the microbiota analysis confirmed that organs had a more substantial impact, explaining 33.9% of the variability, followed by the genetic line, which explained 17.3%. The microbiota of the hepatopancreas was more significantly affected by the genetic line than the intestine. Gen1 exhibited higher richness, diversity, niche breadth, and abundance of beneficial microbes than Gen2, suggesting that Gen1 had a more generalist microbiota. By comparing the microbiota of another set of healthy and diseased shrimps, we confirmed that a higher presence of beneficial microbes was linked to a healthy shrimp status. Additionally, we genotyped and determined the microbiota of wild-type shrimps, proving that they differ from those observed in both genetic lines. Interestingly, ponds with Gen1 had better productivity than Gen2, suggesting a potential link between higher productivity and the microbiota selected by Gen1. Our study highlights the importance of the holobiome perspective in breeding and management programs. It suggests that a specific genetic line and its associated microbiota could be used to select the larvae to be cultivated, improving shrimp aquaculture production.