Data_Sheet_1_Weaning Alters Intestinal Gene Expression Involved in Nutrient Metabolism by Shaping Gut Microbiota in Pigs.docx

Weaning transition usually impairs intestinal architecture and functions and results in gut-associated disorders in pigs. Understanding the changes in intestinal transcriptome and gut microbiota during weaning transition is important for elucidating the underlying mechanism of weaning stress. In the present study, we performed RNA-seq to determine the changes in intestinal transcriptome and 16S rRNA sequencing to measure the gut microbiota changes in the weaning transition. Transcriptome results indicated that weaning transition altered intestinal gene expression involved in nutrient transport and metabolism. Regarding fatty metabolism, fatty acid-binding protein 1 (FABP1), acyl-CoA dehydrogenase (ACADSB), and carnitine palmitoyltransferase 2 (CPT2) expression in the intestine was decreased by weaning. Genes related to bile acid metabolism were increased by weaning, including FABP6, farnesoid X receptor (FXR or NR1H4) and organic solute transporter-α (SLC51A). In addition, genes associated with oxidative stress were altered by weaning transition, including decreased catalase (CAT) and lactate dehydrogenase (LDHA) and increased glutathione peroxidase 2 (GPX2) and superoxide dismutase 3 (SOD3). Results of microbiota composition showed that the Firmicutes abundance and Firmicutes/Bacteroidetes ratio were increased and that the Proteobacteria abundance in the fecal microbiota was decreased by the weaning process; during the weaning transition, the Bacteroides and Fusobacterium abundances decreased markedly, and these bacteria nearly disappeared, while the Prevotella abundance showed a marked increase. Moreover, the levels of the microbial metabolites butyrate and acetate increased with changes in gut microbiota composition. In addition, predictive metagenome by PICRUSt analysis showed that the pathways related to D-glutamine and D-glutamate metabolism, citrate cycle (TCA cycle), peroxisome proliferators-activated receptor (PPAR) signaling, alpha-linolenic acid metabolism were decreased and the pathway related to retinol metabolism was increased in the gut microbiota of piglets during weaning transition. Our results showed that early weaning alters intestinal gene expression involved in nutrient metabolism, which may be due to the changes in microbiota composition.

仔猪断奶过渡期通常会损害肠道组织结构与生理功能，进而引发猪肠道相关疾病。阐明断奶过渡期内肠道转录组（intestinal transcriptome）与肠道菌群（gut microbiota）的动态变化，对于揭示断奶应激的潜在作用机制具有重要价值。本研究通过RNA-seq技术分析断奶过渡期仔猪的肠道转录组变化，并借助16S rRNA测序技术检测肠道菌群的动态改变。转录组测序结果显示，断奶过渡期会调控参与营养物质转运与代谢的肠道基因表达谱。在脂代谢层面，断奶可下调肠道内脂肪酸结合蛋白1（FABP1）、酰基辅酶A脱氢酶（ACADSB）以及肉碱棕榈酰转移酶2（CPT2）的表达水平；与胆汁酸代谢相关的基因则因断奶而上调，包括脂肪酸结合蛋白6（FABP6）、法尼醇X受体（FXR/NR1H4）以及有机溶质转运蛋白-α（SLC51A）。此外，断奶过渡期还会改变与氧化应激相关的基因表达：过氧化氢酶（CAT）与乳酸脱氢酶（LDHA）的表达水平显著下调，而谷胱甘肽过氧化物酶2（GPX2）与超氧化物歧化酶3（SOD3）的表达水平则明显上调。菌群组成分析结果显示，断奶过程可提升粪便菌群中厚壁菌门（Firmicutes）的相对丰度以及厚壁菌门/拟杆菌门（Firmicutes/Bacteroidetes）的比值，同时降低变形菌门（Proteobacteria）的相对丰度；在断奶过渡期内，拟杆菌属（Bacteroides）与梭杆菌属（Fusobacterium）的相对丰度显著下降，几乎完全消失；而普雷沃氏菌属（Prevotella）的相对丰度则显著升高。此外，随着肠道菌群组成的改变，微生物代谢产物丁酸与乙酸的含量也随之上升。通过PICRUSt分析进行宏基因组功能预测的结果显示，断奶过渡期仔猪肠道菌群中，参与D-谷氨酰胺与D-谷氨酸代谢、三羧酸循环（citrate cycle, TCA循环）、过氧化物酶体增殖物激活受体（PPAR）信号通路以及α-亚麻酸代谢的通路丰度下调，而视黄醇代谢通路的丰度则上调。本研究结果表明，早期断奶会调控参与营养物质代谢的肠道基因表达，这一现象可能与肠道菌群组成的改变密切相关。