International Journal of Marine Science, 2026, Vol.16, No.4, 255-270 http://www.aquapublisher.com/index.php/ijms 259 parahaemolyticus was specifically tested with shrimp aquaculture water and designed around field deployment (Rahman et al., 2022; Pu et al., 2026). Flow cytometry offers a different advantage: it rapidly measures phenotypic distributions of microbial cells without first knowing their taxonomy. Machine-learning analysis has shown that flow-cytometric fingerprints can contain information associated with bacterial community composition, although taxonomic abundance prediction remains imperfect (Heyse et al., 2021). In barramundi hatcheries, FCM and 16S sequencing showed complementary trends, suggesting a feasible future division of labor in which rapid fingerprints flag unusual community states and sequencing is reserved for diagnostic clarification (Figure 1) (Bui et al., 2026). Figure 1 Comparison of major microbial monitoring technologies for marine aquaculture health management 4 Microbial Indicators for Health Assessment in Marine Aquaculture 4.1 Potential pathogenic microorganisms as risk indicators Potential pathogens remain necessary indicators because an increasing pathogen burden can mark rising infection pressure. In marine aquaculture, Vibrio, Photobacterium, and Tenacibaculum are particularly relevant in many fish, shrimp, and shellfish contexts, while Aeromonas and other opportunistic genera are important in particular host and environmental settings. Long-term Sanggou Bay monitoring found seasonal enrichment of potentially pathogenic Vibrio, and experimental shrimp studies show that Vibrio harveyi exposure can restructure the gut community (Deris et al., 2022; Lu et al., 2025). Nevertheless, genus-level detection alone is a weak diagnostic criterion. Different Vibrio lineages have sharply different ecological roles and virulence potential. Oyster hatchery monitoring provides a useful warning: Vibrio groups observed during some larval crashes appeared more likely to respond to deterioration than to initiate it (Cram et al., 2024). Pathogen surveillance should therefore combine abundance, species or strain identity where possible, virulence markers, host signs, and environmental context.
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