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张家超+Rob Knight:趋同进化vs.差异调节-益生菌的适应性突变

时间:2021-07-02 10:13来源:热心肠日报 作者:热心肠日报 浏览次数:
Microbiome
[IF:11.607]

  ① 通过鸟枪法宏基因组+分离株全基因组测序,研究植物乳杆菌HNU082(Lp082)在人、鼠和斑马鱼肠道中的进化适应;

  ② Lp082分布于不同生态位,以相似顺序在同样的时间点获得高度一致的单核苷酸变异SNPs,从而定植并适应不同宿主的肠道选择压力;

  ③ 如获得与基因编码蛋白质内膜相关的SNP等,进化出耐酸性及鼠李糖利用能力;

  ④ 宿主常驻菌群的结构、功能对益生菌引入的反应大相径庭,特别是Lp082的竞争者拟杆菌和双歧杆菌属,累积10-70倍的进化变异。

  Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

  06-30, doi: 10.1186/s40168-021-01102-0

  【主编评语】益生菌在宿主肠道内定植适应的机理尚不清晰,特别是缺乏其遗传进化的体内研究。海南大学张家超团队与UCSD的Rob Knight合作在Microbiome上发表文章,以植物乳杆菌HNU082(Lp082)为益生菌模型菌株,揭示其在不同宿主肠道中高度趋同的适应过程和策略。相反,宿主肠道菌群对Lp082的引入呈现出不同反应与互作。而作为‘暂驻菌’,益生菌的引入对肠道常驻菌群遗传组成的影响常常被忽略。(@solo)


Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

候选益生菌植物乳杆菌HNU082在人类、小鼠和斑马鱼肠道中快速、趋同地进化,但有差别地影响常驻微生物组

10.1186/s40168-021-01102-0

06-30, Article

Abstract:

Background: Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.
Results: We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.
Conclusions: Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.

First Authors:
Shi Huang,Shuaiming Jiang,Dongxue Huo

Correspondence Authors:
Rob Knight,Jiachao Zhang

All Authors:
Shi Huang,Shuaiming Jiang,Dongxue Huo,Celeste Allaband,Mehrbod Estaki,Victor Cantu,Pedro Belda-Ferre,Yoshiki Vázquez-Baeza,Qiyun Zhu,Chenchen Ma,Congfa Li,Amir Zarrinpar,Yangyu Liu,Rob Knight,Jiachao Zhang





 
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