Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages

Microbiota play a pivotal role in holobionts, influencing nutrient intake, growth, and overall health. In this context, microbial dysbiosis of <i>Penaeus stylirostris</i> larvae seem to be associated with huge larval mortalities in hatcheries in New Caledonia. To understand larval dysbiosis establishment, our purpose was to identify bacterial biomarkers, as bioindicators, related to a given larval stage and health condition. To this end, larvae were sampled daily to access their active microbiota through sequencing of the V4 region of the 16S rRNA molecule, while their stage and their health were also observed. We identified three biomarkers strongly related to healthy zoea, and some may act as probiotics or play key roles in larval ontogeny and nutrition. We also found six biomarkers linked to unhealthy zoea and eight related to healthy mysis. Biomarkers were mostly related to diseased shrimps (<i>Lewinella</i>) or healthy shrimps (<i>Cognitishimia</i>, <i>Thalassolituus</i>) or were known to prey on cells (P30B-42), suggesting that the larvae might be battling against detrimental conditions. No biomarker related to unhealthy mysis was identified. Finally, our data showed that bacterial bioindicators could be used as an effective biosurveillance proxy in hatcheries, to monitor larval development, and as an early warning tool to predict rearing outcomes.