基于基因组学的乳酸杆菌色氨酸代谢特异性

Tryptophan metabolism characteristics of lactobacilli based on genomics

摘要:

肠道微生物参与的色氨酸代谢能够产生多种吲哚衍生物促进人体健康。乳酸杆菌作为有益的肠道细菌，部分菌株已经被开发成为重要的益生菌，但大多数菌株的色氨酸代谢能力仍不明晰。本研究旨在利用基因组学方法，通过分析特定功能基因揭示乳酸杆菌色氨酸代谢潜在能力，使快速筛选具备生成特定色氨酸代谢产物能力的菌株成为可能。基于新构建的色氨酸代谢功能基因数据集，分析了从公共数据库下载的我国《可用于食品的菌种名单》中16种2 235株乳酸杆菌基因组序列，结果显示除广布乳杆菌属外，乳酸杆菌菌株具有丰富的色氨酸代谢基因，尤其是吲哚-3乳酸生成相关代谢酶基因，超过92%的菌株具有芳香族氨基酸氨基转移酶(aromatic amino acid aminotransferase, ArAT)、吲哚乳酸脱氢酶(indolelactate dehydrogenase, FLDH)和乳酸脱氢酶(lactate dehydrogenase, LDH)，拷贝数分别为1−11个、1−7个和1−11个，表现出了较高的吲哚-3-乳酸生成潜力。系统发育分析研究了吲哚-3-乳酸生成相关代谢酶ArAT、FLDH和LDH的相似性，结果显示ArAT、FLDH和LDH可以分别聚为3−4个簇，每簇的序列都来自不同菌种的菌株，表明乳酸杆菌的吲哚-3-乳酸生成潜力还受到基因型的影响。本研究通过新构建的色氨酸代谢基因数据集，分析了色氨酸代谢基因尤其是吲哚-3-乳酸代谢基因在乳酸杆菌菌株中的分布和基因的系统发育分析，深入解析了乳酸杆菌色氨酸代谢特征，为利用基因组学方法开发功能菌株提供了理论基础和筛选方法。

Abstract:

The metabolism of tryptophan by gut microbiota can produce a variety of indole derivatives to improve human health. As beneficial bacteria in the gut, some strains of lactobacilli have been developed as probiotics and confirmed to have tryptophan metabolism, while the tryptophan metabolism of most strains remains unclear. The aim of this study is to reveal the potential tryptophan metabolism of lactobacilli using genomic methods, which enables the quick identification of strains with the ability to produce specific tryptophan metabolites. Based on the constructed tryptophan metabolism gene dataset, this study analyzed the genome sequences of 2 235 strains of 16 species of lactobacilli in the List of Strains that Can Be Used in Food in China. The results showed that strains of lactobacilli, except Latilactobacillus, carried rich genes associated with tryptophan metabolism, especially the genes encoding enzymes related to indole-3 lactic acid production. More than 92% of strains carried ArAT, FLDH and LDH with 1–11, 1–7, and 1–11 copies, respectively, showing high indole-3-lactic acid production potential. A phylogenetic tree was conducted to study the sequence similarity of ArAT, FLDH, and LDH encoding enzymes involved in indole-3-lactic acid production. The results showed that ArAT, FLDH, or LDH sequences could be clustered into 3–4 groups, and the gene sequences of each cluster were from different strains, indicating that the indole-3-lactic acid production potential of lactobacilli was influenced by genotypes. In this study, we employed the newly constructed tryptophan metabolism gene dataset to study the distribution and phylogenetic relationship of tryptophan metabolism genes, especially indole-3-lactic acid metabolism genes, in lactobacilli. By characterizing the tryptophan metabolism of lactobacilli, this study provides a theoretical basis and screening method for the development of functional strains by genomics methods.