Shared Temporal Dynamics and High Inter-Individual Variability in Stomach Microbiota of Kuruma Shrimp (penaeus Japonicus) Across Aquaculture Farms

Infectious diseases pose a significant threat to kuruma shrimp (Penaeus japonicus) aquaculture, and oral transmission is considered one of the major infection routes. The stomach, where ingested feed is temporarily retained, is a key site for host-microbe interactions that may influence pathogen establishment. However, the ecological characteristics of stomach microbiota under actual aquaculture conditions remain poorly understood. In this study, we characterized the stomach microbiota of apparently healthy kuruma shrimp reared in four commercial aquaculture farms in Okinawa, Japan, using 16S rRNA gene amplicon sequencing with monthly sampling over 1 year. Bacterial community composition exhibited significant but modest temporal structuring across farms, with samples collected at the same time points showing similar community compositions regardless of farm origin, suggesting that shared environmental factors contribute to seasonal dynamics. The genus Photobacterium persistently dominated the stomach microbiota, and stomach communities were clearly distinct from those of the surrounding pond water. Despite this temporal signal, substantial inter-individual variability was observed. At the genus level, four taxa were consistently detected across samples (Photobacterium, Vibrio, Candidatus Bacilloplasma, and Pseudoalteromonas), though sequence-level diversity across farms limited the number of shared amplicon sequence variants. Species richness fluctuated across sampling periods without consistent changes in community evenness. These findings indicate that the stomach microbiota of kuruma shrimp is shaped by the interplay of shared temporal drivers and strong individual variability, providing an ecological baseline for future studies on pathogen establishment via oral transmission in aquaculture systems.