Department of Bioengineering, University of California, San Diego, La Jolla, USA.
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
Food Microbiol. 2023 Oct;115:104334. doi: 10.1016/j.fm.2023.104334. Epub 2023 Jul 8.
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
乳杆菌科是一类重要微生物的大家族，是食品工业的基础。现在已经有许多乳杆菌科菌株的基因组序列可用，使我们能够对该家族进行全面的泛基因组分析。我们从公共资源中收集了 3591 个高质量的基因组，发现：1）它们包含足够的基因组，可用于对 26 个物种进行泛基因组分析；2）归一化 Heap's 系数 λ（衡量泛基因组开放性的指标）的平均值为 0.27（范围为 0.07 至 0.37）；3）泛基因组开放性与转座子和可移动元件的丰度和基因组位置相关；4）每个物种的泛基因组分为核心、辅助和稀有基因组，突出了物种特异性的特征（如运动性和限制修饰系统）；5）植物乳杆菌（在所研究的 26 个物种中发现的基因组数量最多）的泛基因组包含九个不同的系统发育群；6）基因组挖掘揭示了丰富的已检测到的生物合成基因簇，其功能范围从抗菌和益生菌到食品保存，但约 93%的功能未知。这项研究提供了乳杆菌科家族的首次深入比较泛基因组分析。
