Weaning stress shifts codon use and gut microbes in piglet immune cells

Weaning is one of the most abrupt physiological transitions a young mammal experiences: within days, piglets lose maternal nutrition, switch to solid feed, and face a reshaping gut microbial community. A new study led by Dr. Xin Zong at Zhejiang University, published in Science China Life Sciences, reports that this stress is associated with a coordinated shift toward GC-rich codon usage in both the piglet immune system and its gut bacteria, a pattern that accompanies enhanced translation of key immune genes. The work combines ribosome profiling, RNA sequencing, and 16S rRNA sequencing to link host translational control with microbial ecology during early life.

The team analyzed peripheral blood mononuclear cells from healthy and weaned piglets. RNA sequencing identified 94 upregulated and 219 downregulated genes, while ribosome profiling found 245 genes with increased ribosome occupancy and 60 with reduced occupancy. Translation efficiency analysis revealed 70 genes with increased efficiency and 7,312 with decreased efficiency. Immune genes as a group showed higher ribosome occupancy in weaned animals, and inflammatory mediators including CD82, CCL25, and TNFSF13 displayed significantly increased translation efficiency, indicating that weaning reprograms not only which genes are transcribed but which messenger RNAs are actively translated into protein.

The researchers then examined codon usage bias, the tendency of organisms to prefer certain synonymous codons over others, which can influence how efficiently messenger RNAs are translated. In healthy piglets, codons ending in G or C at the third position (GC3 codons) already showed higher usage bias than A/U-ending codons. After weaning, this preference became stronger. Genes with enhanced translation were enriched for GC3 codons encoding leucine, glutamate, and lysine, and the weaning group showed significantly greater GC3-biased usage than healthy controls, while the overall codon adaptation index did not differ between groups.

Weaning was also accompanied by gut microbial dysbiosis: the microbial dysbiosis index was elevated and alpha diversity was reduced in weaned piglets. Genera enriched in healthy animals, such as Romboutsia, Lactobacillus, and Turicibacter, were associated with AT-rich codon usage patterns, whereas genera expanded under weaning stress, such as Fusobacterium and Streptococcus, were linked to GC-enriched codon profiles. Correlation analysis showed that specific taxa, including Romboutsia sp. and Lachnoclostridium sp., were significantly correlated with the translation efficiency of immune transcripts such as CCL25, CD24, and TNFSF13.

Cross-species relative synonymous codon usage analysis revealed coordinated codon preference between gut microbiota and host immune cells, with host cells and dominant bacterial taxa separating according to healthy versus weaning conditions. In synonymous families encoding glutamate, valine, and lysine, bacteria enriched in healthy piglets tended to favor AT-ending codons, while taxa enriched under weaning stress preferred the corresponding GC-ending codons, mirroring the host codon usage profiles. In cell experiments, supplementation with valine, lysine, or glutamate modestly enhanced cell viability and partially mitigated lipopolysaccharide-induced viability loss, and under inflammatory stimulation these amino acids differentially modulated cytokine expression, including TNF-alpha and IL-1beta.

The authors conclude that weaning stress is associated with a coordinated shift toward GC-rich codon usage in both gut microbes and host immune genes, and that this shift may contribute to enhanced translation of key immune genes. They emphasize that the findings reveal an association, not a causal relationship, between microbiota composition and codon-usage-linked translational regulation. Future studies using antibiotic perturbation, fecal microbiota transplantation, and germ-free or gnotobiotic models will be needed to test causality. The study was supported by the National Natural Science Foundation of China and other national programs, and sequencing data have been deposited in the NCBI Sequence Read Archive under accession PRJNA1067344.

Subject of Research: Codon usage and gut microbiota changes in immune translation during weaning stress in piglets

Article Title: Weaning stress rewires immune translation through GC-rich codons and gut microbes in piglets

Article References: Weaning stress rewires immune translation through GC-rich codons and gut microbes in piglets. Original publication (Bibliographic details unavailable.)

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Keywords: weaning stress, piglets, codon usage bias, GC3 codons, ribosome profiling, translation efficiency, gut microbiota, dysbiosis, immune genes, Ribo-seq, 16S rRNA sequencing, amino acid supplementation