Microbiota play critical roles in the early development and health of marine invertebrates, yet microbial transmission and assembly across life stages remain poorly understood in cephalopods. The golden cuttlefish (Sepia esculenta), an important cephalopod in East Asia, suffers high larval mortality, potentially linked to microbiome instability. Here, we investigated vertical microbial transmission, stage-specific microbial succession, and functional roles of core microbiota during early development of S. esculenta. Using high-throughput 16S rRNA sequencing and culture-based methods, we profiled the microbiota across maternal tissues, as well as embryonic stages and post-hatching larvae (n = 79). Two vertically transmitted core genera, Vibrio and Pseudomonas, persisted from maternal organs to offspring and met prevalence and abundance thresholds (NorCI > 0.1). Stage-specific microbial shifts were also observed, with Aureisphaera dominating early embryonic stages and Mycoplasma, Acinetobacter, and Croceibacter emerging after hatching. Functional predictions revealed enrichment of redox-related pathways in embryos and metabolism-associated functions in larvae. Source tracking demonstrated organ-specific microbial transmission, with skin microbiota and environmental inputs. Culture-based isolation successfully retrieved 176 ASVs and improved taxonomic resolution for 92% of them. Three isolates, Bacillus, Pseudoalteromonas, and Sulfitobacter spp., exhibited antagonistic activity against Vibrio tubiashii, suggesting potential probiotic applications. Overall, our results demonstrate that early-life microbiome establishment in S. esculenta involves both maternal inheritance and stage-specific acquisition, providing insights for microbiome-informed strategies to enhance larval health in cephalopod aquaculture.
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