Early-life core microbiota are associated with postlarval survival of Penaeus vannamei: A meta-analysis

Abstract

Larviculture is critical to the production of Penaeus vannamei, the world's leading farmed shrimp species, but remains constrained by erratic postlarval survival. Although early-life microbiome establishment is increasingly recognized as essential for larval health and survival, microbiome-based hatchery interventions are hindered by limited understanding of larval core microbiota. Here, we synthesized publicly available and self-generated 16S rRNA gene amplicon datasets of larval and rearing-water microbiota from 13 studies encompassing seven major producing regions worldwide to characterize shrimp larval core microbiota, their assembly processes, and their associations with larval survival. Although larval prokaryotic communities exhibited stronger geographic variation than developmental-stage succession, a conserved set of dominant bacterial families, including Roseobacteraceae, Vibrionaceae, Flavobacteriaceae, Moraxellaceae, and Pseudoalteromonadaceae, consistently prevailed across developmental stages and regions. By integrating occupancy, persistence, and ecological network centrality analyses, we demonstrated that common, temporal, and ecological core microbiota differ substantially in composition, diversity, stage specificity, and ecological roles in network stability. Compared with non-core taxa, core taxa were generally assembled more deterministically, irrespective of core category, suggesting stronger host selection and/or more rapid dispersal during microbiome establishment. Core microbiota also generally showed stronger associations with postlarval survival than total communities or non-core taxa, although contrasting survival associations among core members indicated that core microbiota are not ecologically homogeneous. Our work provides the first systematic categorization and characterization of larval core microbiota throughout the shrimp larviculture cycle, offering new insights into the ecological significance of core microbiota and identifying potential universal targets for microbiome-based intervention in shrimp larviculture.