Environmental and Host Associated Microbiota in Whiteleg Shrimp Litopenaeus vannamei Aquaculture: Functional and Taxonomic Insights From 16S rRNA Gene Sequencing

Abstract

Shrimp aquaculture, particularly the farming of Pacific whiteleg shrimp Litopenaeus vannamei (L. vannamei), is a rapidly growing industry in Bangladesh, offering significant economic benefits. However, disease outbreaks remain a critical challenge to sustainable production, emphasizing the need for an in-depth understanding of microbial dynamics within aquaculture ecosystems. This study investigated the microbial diversity and functionality of gills and intestines of whiteleg shrimp along with water and sediment of the culture pond, using 16S rRNA gene sequencing. Quality control analysis returned 2,037,500 sequences which comprised a total of 5831 amplicon sequence variants (ASVs). Rarefaction curves confirmed adequate sampling, revealing the highest microbial diversity in pond sediment and the lowest in the intestine of whiteleg shrimp. Venn diagram revealed 16 common ASVs among all samples, with pond sediment with 4181 unique ASVs which was the highest among the samples. At the phylum level, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were dominant across samples, while genus level analysis highlighted Listeria, Rheinheimera, and Flavobacterium. Interestingly, shrimp intestine and gill samples were dominated by the genus Listeria while in water and sediment samples no single microbial species was dominated. Alpha diversity indices indicated the highest bacterial diversity in pond sediment, followed by pond water, intestine, and gill. This study reveals that shrimp intestines, gills, pond water, and sediment harbor distinct microbial communities with minimal overlap, shaped by strong habitat specific selection. While environmental microbiota support nutrient cycling and water quality, shrimp associated microbiota are specialized for digestion and immune functions as predicted by PICRUSt. The presence of Listeria is a public health concern which urge the implication of biosafety in whiteleg shrimp aquaculture in Bangladesh. This study provides new biological insights into microbial dynamics in L. vannamei farming, highlighting how distinct microbial niches within the aquaculture system contribute to shrimp health and ecosystem stability.