Microbial communities associated with stunted growth syndrome in Penaeus vannamei farming

Stunted growth syndrome (SGS) is an emerging concern in Penaeus vannamei farming in India and globally, with limited information available on the aetiology, despite its significant economic impact on shrimp farming. Among the various contributing factors, microbial communities in the culture environment play an important role. Hence the present study aimed to profile the microbial communities in pond water from both SGS affected and healthy shrimp ponds. Microbial profiling and their functional prediction were carried out using metagenomic shotgun sequencing. Taxonomic classification was performed with Kaiju, while metagenome assembly and functional prediction were conducted using OmicsBox. The taxonomic analysis revealed higher dominance of Oceanospirillum and Vibrio species in SGS-affected pond water, whereas Rhodobacteraceae bacterium and Neptunomonas species were more abundant in healthy pond water. Alpha diversity analysis indicated a greater diversity in the healthy pond water sample, compared to SGS-affected pond water. Distinct indicator taxa were identified in both healthy and diseased samples each showing considerable abundance in their respective conditions. Functional prediction revealed that genes related to amino acid transport and metabolism, cell wall/membrane/envelop biogenesis, as well as energy production and conversion were predominant. The observed differences in microbial diversity, along with the presence of indicator taxa in healthy and diseased samples, provide insights into the potential role of microbial communities in the manifestation stunted growth syndrome. Keywords: Kaiju, Metagenomics, OmicsBox, Stunted growth syndrome, Pacific white shrimp