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Objective The mucosal microbiota of large yellow croaker (Larimichthys crocea) plays a vital role in host health and environmental adaptation. However, differences in the mucosal microbiota composition between wild and cultured populations of large yellow croaker, as well as their assembly mechanisms, remain unclear. This study compared the microbiota composition and characteristics in the skin, gill, and intestine of wild and cultured large yellow croaker, aiming to elucidate the impacts of aquaculture environments on host-microbiota interactions. Methods We employed 16S rRNA gene high-throughput sequencing to analyze the microbiota characteristics in the skin, gill, intestine, and surrounding seawater of wild and cultured large yellow croaker. Key bacterial strains were isolated and characterized. Results Significant divergence of mucosal microbiota was observed between cultured and wild populations. (1) Cultured fish exhibited homogenized mucosal microbiota across the skin, gill, and intestine, whereas wild fish maintained strong tissue-specific microbial signatures. (2) Cultured fish had more unique taxa in the skin (156 vs. 93) and gill (171 vs. 50) but fewer unique taxa in the intestine (118 vs. 253) than wild counterparts. (3) LEfSe revealed enrichment of potential opportunistic pathogens (e.g., Vibrio and Photobacterium) in the skin/gill of wild fish, while myxobacteria (e.g., Haliangium) were specifically enriched in the intestine of cultured fish. (4) Co-occurrence networks demonstrated predominantly cooperative interactions in both groups, yet wild fish microbiota displayed stronger competitive relationships. (5) Lysinibacillus sp. isolated from the mucosal tissue of large yellow croaker demonstrated cross-tissue colonization in cultured populations, exhibiting broad-spectrum antibiotic susceptibility and potential probiotic properties. Conclusion The aquaculture environment significantly reshaped the mucosal microbiota composition, diversity, and interaction networks in large yellow croaker, resulting in reduced microbiota stability and impaired metabolic processes, immune competence, and environmental adaptability of the host. These findings provide critical insights for refining aquaculture practices, developing probiotic resources, and mitigating microbiota dysbiosis in large yellow croaker.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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