BackgroundOyster polypeptide (OP) is a mixture of oligopeptides extracted from oysters through enzyme lysis, separation and purification. OP is associated with immunomodulatory effects, but the underlying mechanisms are not known. Therefore, this study combined 1H‐NMR urinary metabolomics and 16S rRNA gene sequencing of the gut microbiome to determine the immunoprotective mechanisms of OP in rats subjected to cyclophosphamide‐induced immunosuppression.ResultsOP can restored the body weight and the structure of spleen and thymus in cyclophosphamide‐induced immunosuppression rats. OP upregulated the levels of white blood cells (WBCs), hemoglobin (HGB), platelets (PLT), red blood cells (RBCs), immunoglobulin G (IgG), immunoglobulin M (IgM), cytokines such as IL‐6 and TNF‐α, and the numbers of CD3+ and CD4+ T cells in the immunosuppression rats. The 1H‐NMR metabolomics results showed that OP significantly reversed the levels of ten metabolites in urinary, including 2‐oxoglutarate, citrate, dimethylamine, taurine, N‐phenylacetylglycine, alanine, betaine, creatinine, uracil, and benzoate. The 16S rRNA gene sequencing results showed that OP restored the gut microbiome homeostasis by increasing the abundance of beneficial bacteria and reducing the abundance of pathogenic bacteria. Finally combining metabolomics and microbiomics found that taurine an hypotaurine metabolism, also alanine, aspartate and glutamate metabolish were disturbed, but these metabolic pathways were restored by OP.ConclusionThis study demonstrated that OP had immunoprotective effects in cyclophosphamide‐induced immunosuppression rats by restoring key metabolic pathways and the gut microbiome homeostasis. Our findings provides a framework for further research into the immunoregulatory mechanisms of OP and its potential use in drugs and nutritional supplements.This article is protected by copyright. All rights reserved.