Characteristics of intestinal microbiota in the Pacific white shrimp Litopenaeus vannamei differing growth performances in the marine cultured environment

Abstract

The Pacific white shrimp Litopenaeus vannamei is the most widely cultivated shrimp in the world, particularly in Asia. The growth performance is a vital factor in shrimp farming. In the present study, comparisons were made among the bacterial communities in shrimp intestines and the related marine farm sediments that supported different growth performances, based on Miseq sequencing data of the V3-V4 region of 16S rRNA gene. Fifty three phyla were identified with the classifiable sequence. Sequencing data demonstrated a statistically significant diversity in microbiota compositions at the phylum and genus levels. The dominant phyla were Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Verrucomicrobia, and Saccharibacteria. Of which, Actinobacteria and Saccharibacteria were more abundant in the shrimp intestines with a normal growth performance, these phyla may be related with shrimp immunity and digestion. Proteobacteria were more abundant in shrimp intestines with slow growth performance, an increased abundance of Proteobacteria was a potential risk of disease. At the genus level, norank_f__Propionibacteriaceae, Ruegeria, Robiginitalea, unclassified_c__Actinobacteria and norank_f__TM146 exhibited extremely statistically significant differences at 0.001 < P ≤ 0.01 while norank_c__Cyanobacteria exhibited statistically significant differences at 0.01 < P ≤ 0.05 among the four groups. The relative abundances of the intestinal bacterial communities in the normal growth shrimps differed significantly from those in the slow growth shrimps. The Firmicutes/Bacteroidetes ratio in the normal growth shrimp intestines was 3.08/3.31 in comparison with 0.34/6.04 in the slow growth shrimp intestines, which suggests that the normal growth shrimp can absorb the nutrient better than the slow growth shrimp. Overall, this study provides valuable findings on the shrimp intestinal microbiota and helps guide the healthy aquaculture practices.