Microbiota-Driven Codon Usage Bias Modulates Immune Genes Translation During Weaning Stress

Weaning stress represents a significant physiological challenge in early life, leading to immune dysregulation and alterations in gut microbiota. Using ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq), we analyzed the transcriptomic and translational changes in PBMCs from healthy and weaning-stressed piglets. The results demonstrate that weaning stress significantly alters the translation of immune-related genes, particularly affecting the codon usage of key amino acids such as Leucine (Leu), Glutamine (Glu), and Lysine (Lys). Notably, the translation efficiency of immune markers such as IL1A, TNF, CSF1, and CXCL2 was significantly enhanced in the weaning group. Analysis of codon usage revealed a marked preference for GC-rich codons, especially at the third codon position (GC3), in the weaning group, suggesting that stress modulates immune gene translation by promoting the use of GC3 codons. Further analysis showed that the gut microbiota composition plays a critical role in modulating codon usage patterns during weaning stress. Notably, Romboutsia, Lactobacillus and Turicibacter predominated in the healthy group, favoring AT-rich codons, while Fusobacterium and streptococcus were enriched in the weaning group, correlating with shifts to GC-rich codons. This microbial shift influenced translation efficiency, as indicated by higher GC3 content and codon adaptation index in the weaning group. Our findings uncover a novel mechanism by which gut microbiota, through specific microbial interactions with PBMCs, regulates immune gene translation in response to weaning stress. These insights provide a deeper understanding of microbiome-mediated translational regulation and offer potential strategies to improve stress resilience and enhance livestock health management.