Monitoring and prediction of Aeromonas veronii dynamics via absolute quantification microbiome sequencing facilitated the development of a risk assessment tool in a shrimp farm

The outbreak of infectious bacterial diseases in aquaculture is a major concern in the industry. Among those pathogens, Aeromonas species are one of the most important bacterial pathogens of cultured animals. From May to June of 2022, an unexplained Aeromonas veronii outbreak was observed in a shrimp farm with high morbidity and mortality. To develop a risk assessment tool, the dynamics of the microbiome were monitored via absolute quantification of 16S rRNA amplicon sequencing for 18 consecutive days in a recirculating aquaculture system (RAS) for rearing water and the gut of whiteleg shrimp (Litopenaeus vannamei). A growth model was also developed for predicting the growth of Aeromonas in the shrimp gut and rearing water. The results showed that A. veronii is a dominant bacterial strain isolated from sick L. vannamei. The comparison of the bacterial community in the shrimp gut and rearing water over time showed remarkable shifts in A. veronii and probiotic Bacillus in the rearing water, with a significant decline in probiotic Bacillus. The rapid increase in A. veronii in rearing water subsequently altered A. veronii populations in the shrimp gut, with over 80% of A. veronii found on day 18. Linear regression analysis revealed a strong positive relationship between the abundance of A. veronii in the shrimp gut and the rearing water. The growth kinetic model agreed well with the observed values. Collectively, the temporal dynamics of the bacterial community in the rearing water offer valuable information for the fate of administered probiotics and pathogens. Growth kinetic models provide useful information to reduce the abundance of pathogens, which can be used as an early warning tool. These observations offer crucial insights into the dynamics of the bacterial community in shrimp and their environment, which can significantly impact shrimp health and productivity.