Metagenomic Analysis Of Exotic Litopenaeus Vannamei And Rearing Environment

Abstract

Litopenaeus vannamei has rapidly reshaped Indian aquaculture, yet recurrent disease episodes and environmental concerns highlight the need to understand host–environment microbiome linkages. We profiled bacterial communities from shrimp intestines, pond water, and pond sediment collected in Andhra Pradesh (East Godavari) and applied 16S rRNA V3–V4 amplicon sequencing with a standard QIIME/UCHIME pipeline and Greengenes‐based OTU calling, followed by alpha/beta diversity analyses (including unweighted UniFrac PCoA) and LEfSe to resolve habitat-enriched taxa. Across matrices, Proteobacteria constituted the core phylum; gut samples were additionally enriched in Firmicutes and Cyanobacteria, pond sediments in Cyanobacteria, and pond water in Actinobacteria. Genera dominating each niche included Lactococcus (gut), Robiginitalea/Bacillus (sediment), and Pseudoal tero monas/ Macrococcus (water). Notably, gut–environment coupling was strong: 32 genera were shared between gut and sediment and 26 between gut and water, underscoring continuous microbial exchange at the culture interface. The prominence of Lactococcus in intestines—coupled with the non-dominance of Gammaproteobacteria—aligns with healthier culture conditions and suggests scope for targeted probiotic or prebiotic interventions. Beyond production outcomes, our data indicate that large-scale cultivation of an exotic species could mobilize and disseminate non-native microbiota into local waters, warranting strengthened biosecurity and effluent management. Collectively, these results provide a habitat-resolved baseline of Indian L. vannamei microbiomes, identify actionable microbial indicators for husbandry, and frame ecological safeguards for sustainable intensification.