Global in silico analysis reveals a core gut microbiota in fall armyworm ( Spodoptera frugiperda ) shaped by geography and diet

Abstract Fall armyworms (Spodoptera frugiperda) are an invasive agricultural pest whose adaptability and resilience are increasingly linked to their gut microbiota. In this study, we performed a global-scale in-silico meta-analysis of publicly available 16S rRNA datasets to identify a conserved core gut microbiota and assess how geography and diet shape microbial community structure and function. Using both prevalence-based and unsupervised clustering approaches, we defined a robust global core microbiota composed of 88 high-confidence ASVs, including genera such as Enterococcus, Pseudomonas, and Acinetobacter, which were consistently present regardless of geographical region or diet. These taxa are important in nutrient metabolism, detoxification, and stress tolerance, contributing to host fitness and ecological success. Geographic origin significantly influenced gut microbiota diversity and composition, with continent- and country-level differences supported by alpha/beta diversity metrics and supervised machine learning classification (AUC = 1.0). Diet also influenced microbial community structure, although its effect was weaker than that of geography, explaining 11.9% of the variation compared to 13.5%. Functional predictions using PICRUSt2 revealed region-specific enrichment of pathways related to xenobiotic degradation, amino acid metabolism, and vitamin biosynthesis, suggesting specific microbial taxa may contribute to host adaptation and resilience through these metabolic functions. This is the first global synthesis of the S. frugiperda gut microbiota that integrates geographic and dietary factors. The identification of a global-level conserved core microbiota provides a foundation for developing synthetic microbial communities and microbiome-informed pest management strategies aimed at enhancing control efficacy.