Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources

• This study characterized the intestinal microbiota in Litopenaeus vannamei.
• Different lipid sources influenced the intestinal bacterial composition.
• Host phylogeny imposes selective pressure on the microbial community assembly.

Even though the Pacific white shrimp is a very important culture species, there is little information on the effect of feed nutrients on the intestinal microbiota. In shrimp, dietary fatty acids largely affect the growth and immune system of Litopenaeus vannamei in part by changing the intestinal bacterial profile. Therefore, an Illumina-based sequencing method was used to examine the intestinal bacterial composition of L. vannamei following six diets with different lipid sources. The bacterial communities in the culture water and shrimp intestinal contents were also compared. The results revealed that shrimp fed a diet with an equal combination of soybean oil, beef tallow, and linseed oil (SBL) had significantly higher weight gain and survival rate than those fed with soybean oil or beef tallow. Proteobacteria and Tenericutes were dominant in the intestines of L. vannamei regardless of the diet. There was a significant prevalence of Rhizobiaceae in shrimp fed the SBL diet than in shrimp fed diets with soybean oil or beef tallow. Proteobacteria dominated in both the culture water and shrimp intestinal samples of L. vannamei. These results suggest that the host intestinal environment imposes selective pressure on the establishment of microbial communities. Lipid sources with different fatty acid compositions could affect the composition of the intestinal microbiota of L. vannamei.