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Aims This study explores the impact of gut microbiota on body metabolites and the growth rate of sea cucumber seedlings. Methods and results A comprehensive analysis using metabolomics and microbiomics was conducted to ascertain the gut microbiota and body metabolites in sea cucumber seedlings exhibiting varying growth rates. Distinct changes in the intestinal flora were observed in correlation with different growth rates of sea cucumber seedlings. The microbial communities of faster-growing seedlings exhibited greater diversity and evenness of taxa. For example, the abundance of genera Rhodococcus, Woeseia, Lysobacter, Desulfuromonadia_Sva1033 , and Flavobacteriaceae_NS5_marine_group was more than 24 times higher in the fast-growing group compared to the slow-growing group. Metabolomics analysis revealed an association between high growth rates of cucumber seedlings and discrepancies in metabolites, such as amino acids, lipids, and carbohydrates. Isorenieratene, possibly synthesized by Rhodococcus , was more than 2.5 times more abundant in the fast-growing group than the slow-growing group. Slow-growing seedlings showed considerable enrichment of environmental pollutants, such as antibiotics and drugs, while their colonies were devoid of bacteria capable of degrading such pollutants. In addition, significant differences were observed between groups in the biosynthesis of amino acids, metabolism of arginine and proline, biosynthesis of unsaturated fatty acids, and metabolism of linoleic acid. Moreover, significant correlations between the microbial genera and sea cucumber metabolites were identified through correlation analysis. Conclusions Significant differences exist in the gut microbiota and metabolite composition among seedlings with varying growth rates. Microbes residing in the gut have the potential to influence the growth of seedlings through modulation of their metabolism. [ABSTRACT FROM AUTHOR]