Comparative genomic analysis of 455 Lactiplantibacillus plantarum isolates: Habitat-specific genomes shaped by frequent recombination
Comparative genomic analysis of 455 Lactiplantibacillus plantarum isolates: Habitat-specific genomes shaped by frequent recombination
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DOI：
10.1016/j.fm.2022.103989
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发表时间：
2022-01-21
影响因子：
5.3
通讯作者：
Zhang, Wenyi
中科院分区：
文献类型：
--
作者：
Li, Kangning;Wang, Shaojing;Zhang, Wenyi
对455株乳酸杆菌（Lactiplantibacillus（L.）plantarum genomes基因组。本研究首先利用L. plantarum，系统发育树包括两个主要分支。进化枝B中的菌株比进化枝A中的菌株遗传多样性更高。此外，在L. B分支内还鉴定出了12个菌株的单分支（分支B1）。植物值得注意的是，这12个菌株来自不同的生态位和广泛的地理区域。植物相关的菌株均匀分布在整个系统发育树。而乳制品来源的菌株主要分布在分支B，而动物源和肉制品来源的菌株主要分布在分支A。所有455 L的总体r/m比（重组和突变事件的比率）。植物分离物（1.181）的r/m值远低于分支B1（5.510），动物分离物（0.607）和分支B（4.373）的r/m值相差7倍。乳制品和动物源分离物具有多个环境特异性基因。我们的研究结果加深了对L.植物
A large-scale comparative genomic analysis together with genome-wide association study of 455 Lactiplantibacillus (L.) plantarum genomes was performed. Firstly, the study generated phylogenic tree using core-genome of L. plantarum, and the phylogenetic tree comprised two major clades. The isolates in clade B were genetically more diverse than those of clade A. Furthermore, a mono-clade (clade B1) of 12 isolates was identified within clade B in L. plantarum. It is interesting to note that these 12 isolates were originated from diverse niches and wide geographic regions. Plant-associated isolates were distributed evenly across the phylogenetic tree. In contrast, more dairy product-originated isolates were distributed in clade B, while the animal- and meat productoriginated isolates located mainly in clade A. The overall r/m ratio (ratio of recombination and mutation events) of all 455 L. plantarum isolates (1.181) was a lot lower than that of clade B1 (5.510), and there was a seven-fold difference in the r/m ratio between animal-originated isolates distributed to clade A (0.607) and clade B (4.373). The dairy and animal-originated isolates possessed multiple environment-specific genes. Our findings deepen the understanding of the niche-specific genome diversity of L. plantarum.