比较基因组学分析不同来源罗伊氏乳杆菌基因多样性及生境适应性

Comparative genomics analysis of genetic diversity and habitat adaptability of Lactobacillus reuteri from different sources

摘要:

[目的]研究34株不同来源罗伊氏乳杆菌（Lactobacillus reuteri）基因多样性及生境适应性机制，了解该菌株在肠外生境及肠内生境中适应性的异同，为L.reuteri优良菌株的开发提供理论基础。[方法]基于二代测序平台对11株源于发酵食品（酸马奶、酸粥）的L.reuteri进行测序，并应用比较基因组学将其与发酵食品、酸面团、食草动物L.reuteri分离株基因组进行比较分析。[结果]分离自酸马奶、酸粥L.reuteri基因组大小平均为2.14 Mb，GC含量平均为38.77%，且同种来源分离株系统发育关系距离较近。泛-核心基因集分别包含7242个、969个基因家族，其中酸马奶分离株特异性基因最多为459个。功能注释结果显示不同来源菌株碳水化合物、氨基酸相关基因数量及种类差异较大，仅在发酵食品和食草动物株中发现抗生素耐药性基因。注释到的碳水化合物活性酶中仅出现在发酵食品与食草动物分离株的为GH3（β-葡萄糖苷酶等）和GH43（β-木糖苷酶等），特有的分别为AA3（纤维二糖脱氢酶等）和GH66（葡萄糖转移酶等）。[结论]不同来源L.reuteri具有广泛的基因多样性，与生存环境密切相关。发酵食品分离株具有部分食草动物肠道菌株特性且具有其独特的环境适应性特征，体现了与宿主有关的环境适应能力，可加深对食品发酵和肠内环境中细菌生境适应性的理解。

Abstract:

[Objective] We studied the genetic diversity and habitat adaptability mechanism of 34 strains of Lactobacillus reuteri from different sources. We aimed to compared the differences of their adaptability in extraintestinal and intraintestinal habitats to provide theoretical basis for the development of Lactobacillus reuteri strains. [Methods] Based on the second generation sequencing platform, We sequenced 11 Lactobacillus reuteri strains from fermented food (yogurt and sour porridge) and compared with the genomes of fermented food, sour dough and herbivore sources of Lactobacillus reuteri strains by comparative genomics. [Results] The average genome size and GC content of L. reuteri isolated from yoghurt and sour porridge were 2.14 Mb and 38.77% respectively, and the phylogenetic relationship between the isolates from the same source was close. Pan-core gene sets consisted of 7242 and 969 gene families, yoghurt isolates had the most specific genes (459). Functional annotation showed that the number and types of carbohydrate and amino acid related genes varied greatly among strains from different sources, and the antibiotic resistance genes were found only in fermented food and herbivores strains. The carbohydrate-active enzymes of GH3 (β-glucosidase etc.) and GH43 (β-xylosidase etc.)only appeared in fermented food herbivore isolates, and the specific ones were AA3 (cellobiose dehydrogenase etc.) and GH66 (dextranase etc.), respectively. [Conclusion] Lactobacillus reuteri from different sources has a wide range of genetic diversity and is closely related to the living environment. Fermented food isolates had the characteristics of some herbivorous intestinal strains and their unique environmental adaptability, and reflected the host environmental adaptability. It can deepen the understanding of food fermentation and bacterial habitat adaptability in intestinal environment.