The mammalian intestine harbors heterogeneous distribution of microbes among which specific taxa (e.g. Lactobacillus) dominate across mammals. Deterministic factors such as nutrient availability and utilization may affect microbial distributions. Due to physiological complexity, mechanisms linking nutrient utilization and the dominance of key taxa remain unclear. Lactobacillus amylovorus is a predominant species in the small intestine of pigs. Employing a pig model, we found that the small intestine was dominated by Lactobacillus and particularly L. amylovorus, and enriched with peptide-bound amino acids (PBAAs), all of which were further boosted after a peptide-rich diet. To investigate the bacterial growth dominance mechanism, a representative strain L. amylovorus S1 was isolated from the small intestine and anaerobically cultured in media with free amino acids or peptides as sole nitrogen sources. L. amylovorus S1 grew preferentially with peptide-rich rather than amino acid-rich substrates, as reflected by enhanced growth and PBAA utilization, and peptide transporter upregulations. Utilization of free amino acids (e.g. methionine, valine, lysine) and expressions of transporters and metabolic enzymes were enhanced simultaneously in peptide-rich substrate. Additionally, lactate was elevated in peptide-rich substrates while acetate in amino acid-rich substrates, indicating distinct metabolic patterns depending on substrate forms. These results suggest that an increased capability of utilizing PBAAs contributes to the dominance of L. amylovorus, indicating amino acid utilization as a deterministic factor affecting intestinal microbial distribution. These findings may provide new insights into the microbe-gut nutrition interplay and guidelines for dietary manipulations toward gut health especially small intestine health.

哺乳动物肠道中微生物分布不均匀，其中特定的分类群（例如乳酸杆菌）在哺乳动物中占主导地位。诸如养分可用性和利用等确定性因素可能会影响微生物的分布。由于生理复杂性，将营养利用与关键类群优势联系起来的机制仍不清楚。淀粉乳杆菌是猪小肠中的优势菌种。使用猪模型，我们发现小肠以乳酸杆菌为主，尤其是L. amylovorus，并富含肽结合氨基酸（PBAAs），在富含肽的饮食后，所有这些都得到了进一步的提升。为了研究细菌生长优势机制，从小肠中分离出代表性菌株L. amylovorus S1，并在以游离氨基酸或肽作为唯一氮源的培养基中厌氧培养。淀粉乳杆菌S1 优先使用富含肽而不是富含氨基酸的底物生长，这反映在增强的生长和 PBAA 利用率以及肽转运蛋白上调。在富含肽的底物中，游离氨基酸（例如蛋氨酸、缬氨酸、赖氨酸）的利用以及转运蛋白和代谢酶的表达同时得到增强。此外，乳酸在富含肽的底物中升高，而乙酸在富含氨基酸的底物中升高，表明不同的代谢模式取决于底物形式。这些结果表明，提高利用 PBAAs 的能力有助于L. amylovorus的优势，表明氨基酸利用是影响肠道微生物分布的决定性因素。这些发现可能为微生物-肠道营养相互作用和肠道健康特别是小肠健康的饮食操作指南提供新的见解。