Profiling the gut microbiome of Pacific Whiteleg shrimp, Litopeneaus vannamei raised in an indoor biofloc aquaculture system

Understanding the microbial composition and functionality within the gut system of cultured organisms provide crucial information about nutrient utilisation and immunity potentials. This study investigated the gut microbiome of Litopenaeus vannamei cultured in an indoor biofloc aquaculture system. The research aimed to evaluate the influence of biofloc treatments on microbial diversity and abundance within shrimp guts essential for their defence system. Shrimp were raised under three treatment conditions namely, a control (non-biofloc) and two biofloc setups. The biofloc treatment comprised GRG1 (200 shrimp/m³, C/N ratio of 10, probiotic dosage 14 ml/L) and GRG2 (200 shrimp/m³, C/N ratio of 20, probiotic dosage 7 ml/L). Ten gut samples of shrimp from each group were analysed using 16S rRNA gene sequencing to characterize the microbial communities. Biofloc-treated groups, particularly GRG2, showed substantially higher abundances of beneficial microbes, such as Fusobacteriaceae and Peptostreptococcaceae. The microbial family Fusobacteriaceae reached a relative abundance of 0.79 in GRG2 and 0.32 in GRG1, compared to 0.03 in the control group. Also, the presence of Bacteroidetes and Photobacterium further indicated a favourable microbial shift in biofloc treatments. It was concluded that biofloc positively influenced the gut microbiome by enhancing microbial diversity and promoting beneficial microbial populations that could improve the shrimp health and aquaculture productivity. These findings underscore the potential of biofloc to enhance digestive efficiency and immune function in shrimp.