Metagenomic profiles of core and signature bacteria in the guts of white shrimp, Litopenaeus vannamei, with different growth rates

Abstract

A large number of studies have previously revealed evidence suggesting a strong correlation between gut bacteria and the growth performance of aquatic animals. However, specific research reporting bacterial communities inhabiting white shrimps with different growth rates are still very limited. Thus, the present study aimed at investigating the structure and composition of core and signature bacteria in the gut of shrimps at different growth rates. A total of 60 healthy white shrimps, Litopenaeus vannamei, with different growth rates (slow vs fast) were collected from three shrimp ponds as replicates. Bacterial 16S rRNA genes associated with these shrimp guts were extracted, amplified and sequenced using next-generation sequencing (NGS) analysis to determine the structure and composition of the bacterial community within and between groups. The result showed that 35 genera of 181 detected genera (19.34%) were considered to be the core microbiome in the gut of white shrimps regarding their prevalence in all samples including Illumatobacter, Ruegeria, Candidatus Bacillopora, Roseovarius, Silicimonas, Algoriphagus, Haloferula, Dinoroesobacter, Vibrio, Lactobacillus, Bdellovibrio, Shimia, and Robiginitalea. In addition, there was a strong association between diversity and species richness of gut bacteria and the growth of white shrimps. The species richness and the Shannon index representing bacterial diversity were significantly lower in the fast-growing shrimps (p < 0.05), reinforcing the close relationship between gut bacteria and their host growth. Further analysis using linear discriminant analysis effect size (LEfSe) indicated that nine bacterial species were significantly higher in the fast-growing shrimps (Group 1) than the slow-growing shrimps (Group 2). The nine species were identified as Coprococcus comes (OTU58), Oscillibater sp. ER4 (OTU74), Acidaminicoccus intestini (OTU210) and Bacteroidetes ovatus (OTU671), Oscilibacter sp. (OTU274), Peptococcus sp. (OTU218), Clostridium phoceensis (OTU313), Legionella sp. (OTU682), and unidentified Clostridiales (OTU186). These results might suggest that the nine bacterial species are bacterial signatures for the high growth shrimps. However, due to the novelty of the shrimp gut bacteria, further studies are still required to understand their specific roles and contribution to the growth of white shrimps.