Consistent features of the gut microbiota in response to diverse shrimp Litopenaeus vannamei diseases: A meta-analysis

Abstract

Dysbiosis in the gut microbiota has been intimately implicated in shrimp (Litopenaeus vannamei, Penaeidae) diseases. However, considering the variety of shrimp diseases and the variability in experimental conditions, studies addressing common features of the gut microbiota−shrimp disease relationship are limited. Through an unbiased subject-level meta-analysis framework, 463 shrimp gut bacterial communities from 27 studies were re-analysed, including six lifestages and eight diseases of shrimp, with the causal agents of viral, bacterial, eukaryotic, and unknown pathogens. Shrimp lifestages and diseases were the predominant factors governing the gut microbiota. After ruling out the top lifestage- and disease-specific discriminatory amplicon sequence variants (ASVs) from the gut microbiota, the top 27 disease common-discriminatory ASVs were identified, contributing to an overall accuracy of 95.9% in diagnosing shrimp health status. By using these optimisation procedures, the accuracy of our diagnosis model was unbiased by shrimp lifestage, specific disease, sampling size, hypervariable region and sequencing platform. The shrimp eight diseases consistently and significantly increased the relative importance of stochasticity, the relative abundance of pathogenic potentials and diversified core ASVs, whereas decreased the diversity and stability of gut microbiota. Collectively, these findings illustrate the effectiveness of meta-analysis in determining the robust and common features of the shrimp gut microbiota in response to diverse diseases. In particular, disease common-discriminatory ASVs could accurately diagnose shrimp health status, although the data are divergent in biotic and technical variances.