A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.
A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.
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低成本的基因组工作流程可实现微生物组中的分离筛选和应变水平分析。
DOI：
10.1186/s13059-022-02777-w
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发表时间：
2022-10-12
期刊：
影响因子：
12.3
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中科院分区：
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作者：
地球环境中蕴藏着复杂的微生物群体，它们影响着从宿主健康到生物地球化学循环的各种过程。由于无法以高通量的方式分离基因组，对它们的进化和功能的理解受到限制。在这里，我们介绍了一种使用开源实验室软件和OpenTrons机器人平台进行细菌全基因组测序的工作流程，将成本降低到每个基因组大约10美元。我们评估了来自野生黑猩猩和矮黑猩猩的45种肠道细菌的基因组多样性。我们量化了种内基因组多样性，并揭示了寄主之间同源质粒的差异。这使得对细菌菌株的群体遗传分析目前仅靠元基因组数据是不可能的。网上版载有补充材料，可在10.1186/s13059-022-02777-w查阅。
Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone. The online version contains supplementary material available at 10.1186/s13059-022-02777-w.