Porcine gut loops to explore the impact of amino acids on the host–microbiota crosstalk in the ileum

Amino acids (AAs) are essential for the growth, development, and health of pigs, yet their direct effects on the intestinal barrier and microbiota remain poorly understood in vivo , despite extensive in vitro studies on mucosal barrier integrity. While intestinal cell lines and organoids provide valuable insights, they cannot fully capture the complexity of the in vivo intestinal mucosa, where diverse cell types interact dynamically with each other and the microbiota. To address this gap, we hypothesized that the ligated intestinal loop model could serve as an intermediate system, clarifying the effects of AAs on the intestinal mucosa and microbiota while reducing the need for experimental animals. This study aimed to test this surgical approach for the first time, assessing the short-term impact of AA administration and laying the groundwork for future model optimization. We prepared ten ileal loops in four weaned pigs and administered either PBS, lysine (3 g/L), a mixture of branched-chain AAs (3 g/L), or tryptophan (3 g/L) for 48 h. Subsequent analyses of loop content metabolites, microbiota composition, and mucosal gene expression revealed that gene expression, metabolic, and microbial profiles were primarily driven by interindividual variability among pigs. Although no statistically significant differences were detected between treatment groups, several trends were identified. While the intestinal loop model shows potential for short-term assessments of AA mixtures on the intestinal mucosa and microbiota, further optimization is needed to fully realize its potential.