Bacterial community diversity, abundance, and composition of rearing water and red tilapia gills from open river cages and earthen ponds in Central Thailand

Tilapia, a valuable fish species, ranks as the world’s second-largest farmed fish. In Thailand, it is a prominent cultured species, specifically the red tilapia hybrids (Oreochromis spp.). Understanding the factors influencing tilapia’s microbiome is essential to mitigate fish mortality and production decline. The study assesses the rearing water and fish gill microbiome in red tilapia culture, comparing closed earthen pond and open river cage culture systems across five provinces in Central Thailand. We conducted 16S rRNA amplicon sequencing (V3-V4 hypervariable regions) on bacterial DNA from 30 gills and 27 rearing water samples The results revealed that the location had a more significant impact (p < 0.05) than the culture system on both gills and water microbiomes. No association between abiotic factors and gill microbiome diversity was observed, while significant associations were observed between the water microbiome with ambient temperature (Ta) (p < 0.00), water temperature (Tw) (p < 0.00), pH (p < 0.03), and salinity (p < 0.01). Fish pathogens such as Streptococcus agalactiae and Mycobacterium spp. were consistently among the top 5 most abundant bacteria found in both water and fish gill samples across all provinces. Furthermore, several significant fish pathogens, including Vibrio spp., Aeromonas hydrophila, Flavobacterium spp., and Edwardsiella spp., which pose a threat to public health and food safety and security, were detected, albeit in relatively low abundance (< 0.04