Bacterial microbiota of African catfish Clarias gariepinus during the hatchery and nursery phases of culture in the Philippines

Abstract

The bacterial microbiota of African catfish (<i>Clarias gariepinus</i>) during hatchery and nursery phases were examined across eight production cycles in two commercial farms in the Philippines. Bacterial identification was performed using conventional methods and the API 20E test, with further confirmation of selected isolates via 16S rRNA gene sequencing. Heterotrophic plate count (HPC), presumptive <i>Aeromonas</i> count (PAC), and presumptive <i>Vibrio</i> count (PVC) varied in hatchery rearing water (10³–10⁵ CFU/mL for HPC; 10²–10⁴ CFU/mL for PAC and PVC) and fry samples (10⁴–10⁷ CFU/g for HPC; undetectable–10⁶ CFU/g for PAC; 10²–10⁴ CFU/g for PVC). In the nursery phase, similar fluctuations were observed in rearing water, fingerlings, and sediment. Microbial diversity analysis revealed 21 species (15 genera) in hatchery rearing water and 14 species (8 genera) in fry, with <i>Aeromonas hydrophila</i>, <i>A. sobria</i>, and <i>Vibrio cholerae</i> as predominant species (>15%). In the nursery phase, 29 species (16 genera), 28 species (15 genera), and 21 species (14 genera) were identified from rearing water, sediment, and fingerlings, respectively, with <i>A. hydrophila</i>, <i>A. sobria</i>, and <i>Bacillus subtilis</i> dominating (>14%). This study highlights the dynamic composition of bacterial communities in catfish culture systems, with rearing environments shaping the microbiota of juvenile fish. The presence of opportunistic and zoonotic pathogens underscores the risk of disease outbreaks, particularly under suboptimal conditions. These findings emphasize the need for stringent biosecurity measures and improved hatchery and nursery management practices to enhance fish health, prevent economic losses, and ensure the sustainability of aquaculture production. Educating hatchery and nursery workers on safe aquaculture practices and hygiene protocols is crucial to minimizing health risks to both fish and humans while ensuring efficient and responsible catfish production.