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Microplastics (MPs) are a hazardous pollutant of world concern that threaten aquatic organisms and ecosystems. In this study, we chose the worldwide-distributed shrimp Litopenaeus vannamei as a model and investigated the toxicological effects of five types of MPs on L. vannamei using several omics approaches. After 14 days of exposure to MPs, obvious intestinal microbiota variation was observed, such as increased abundances of Bacteroidetes and Proteobacteria and a decreased abundance of Firmicutes. Specifically, MPs induced several putative opportunistic pathogens and reduced lactic acid- and short-chain fatty acid-producing bacteria. Alternatively, MPs altered haemolymph proteome profiles, but the five types of MPs had different effects on the enriched pathways and the expression of immune-related proteins. Furthermore, MPs also caused haemolymph metabolite variation, especially in amino acid and alpha-linolenic acid metabolism, and 28 differential metabolites were altered in the five MP-treated groups. Changes in intestinal bacteria were correlated with the haemolymph proteins and metabolites of the shrimp. Overall, these results reveal the toxicological effects of MPs on the intestinal microbiota and the host's immunity and metabolism in shrimp. Unlabelled Image • Intestinal microbiota and haemolymph protein and metabolite molecules were affected. • Intestinal lactic acid and short chain fatty acid producing bacteria abundance were decreased. • Different types of MPs changed haemolymph protein profiles differently. • Haemolymph amino acids and alpha-linolenic acid metabolism were altered. • Several stress-related protein and metabolite markers were identified. [ABSTRACT FROM AUTHOR]