Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
Gombe Stream Research Center, Kigoma, Tanzania.
Genome Biol. 2022 Oct 12;23(1):212. doi: 10.1186/s13059-022-02777-w.
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.
地球环境中存在着复杂的微生物群落，这些微生物影响着从宿主健康到生物地球化学循环等各种过程。由于无法以高通量的方式分离基因组，因此对它们的进化和功能的理解受到了限制。在这里，我们展示了一种使用开源实验室设备和 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约 10 美元。我们评估了来自野生黑猩猩和倭黑猩猩的 45 种肠道细菌物种的基因组多样性。我们量化了种内基因组多样性，并揭示了宿主之间同源质粒的分歧。这使得对目前仅通过宏基因组数据无法进行的细菌菌株的种群遗传分析成为可能。
