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    張家超+Rob Knight:趨同進化vs.差異調節-益生菌的適應性突變

    發布日期:2021-07-12
     ?、?通過鳥槍法宏基因組+分離株全基因組測序,研究植物乳桿菌HNU082(Lp082)在人、鼠和斑馬魚腸道中的進化適應;

     ?、?Lp082分布于不同生態位,以相似順序在同樣的時間點獲得高度一致的單核苷酸變異SNPs,從而定植并適應不同宿主的腸道選擇壓力;

     ?、?如獲得與基因編碼蛋白質內膜相關的SNP等,進化出耐酸性及鼠李糖利用能力;

     ?、?宿主常駐菌群的結構、功能對益生菌引入的反應大相徑庭,特別是Lp082的競爭者擬桿菌和雙歧桿菌屬,累積10-70倍的進化變異。

      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

      【主編評語】益生菌在宿主腸道內定植適應的機理尚不清晰,特別是缺乏其遺傳進化的體內研究。海南大學張家超團隊與UCSD的Rob Knight合作在Microbiome上發表文章,以植物乳桿菌HNU082(Lp082)為益生菌模型菌株,揭示其在不同宿主腸道中高度趨同的適應過程和策略。相反,宿主腸道菌群對Lp082的引入呈現出不同反應與互作。而作為‘暫駐菌’,益生菌的引入對腸道常駐菌群遺傳組成的影響常常被忽略。(@solo)


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

    候選益生菌植物乳桿菌HNU082在人類、小鼠和斑馬魚腸道中快速、趨同地進化,但有差別地影響常駐微生物組

    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

      來源:網絡


     
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