Crustaceans are the second main aquaculture product farmed worldwide, being the white leg shrimp (Litopenaeus vannamei), the most valuable species. Despite its successful production, shrimp may be the aquaculture species most impacted by the disease. There is growing evidence that the structure and composition of its microbiota is an essential factor for its health condition. Nevertheless, the relationship between the host genotype of L. vannamei shrimp populations with its microbiota is unexplored. To determine this relationship, we used 16S rRNA amplicon sequencing to characterize the gut and hepatopancreas microbiota and genotypification with Illumina Infinium ShrimpLD-24 v1.0 of two populations of L. vannamei shrimps collected from three different ponds of a shrimp hatchery in México.
The organ and genotype were the main factors shaping the shrimp microbiota. With the principal coordinate analysis (PCoA) using Unweighted UniFrac distances, we observed a clear separation between samples tagged by organ (Fig. 1A) and by genetic lines (Fig. 1B). Additionally, ANOSIM analysis showed that organ was the most important factor shaping the microbial structure, followed by the genetic line.
A genetic line drove microbiota richness and diversity. We found differences between Gen 1 and Gen 2 groups; this can be observed with the Chao1 index (Fig. 1C) and the Shannon index (Fig. 1D), respectively.
Genetic line influences the abundance of probiotics. Probiotics were increased in healthy as compared to diseased samples, in the same way, there was a significant enrichment of probiotic species in Gen1 compared to Gen2, independently of the organ (Fig. 1E) , which implies a possible selection of probiotics from the genetics of the host that could impact in its health status.