Advancing microbiome science with long-read sequencing

微生物是支撑地球和人类健康的“微型化学工厂”。尽管地球上的大多数生物多样性都保存在单细胞微生物中，但我们无法在实验室培养绝大多数微生物，这对我们研究这些微生物的能力构成了挑战。因此，过去几十年来基因组测序技术的进步支持了对微生物群落在其原位生境或微生物群中的研究。这些高通量测序技术能够通过应用元基因组学对微生物群进行原位研究，这涉及到对环境DNA进行大量测序，以重建高质量的微生物基因组，和/或通过高通量基因扩增子测序。微生物组科学的最新发现使与人类健康、海洋营养循环以及环境污染治理和控制有关的新理论成为可能。尽管有这样的突破，传统的DNA测序技术在其允许的读取长度方面仍然有一个关键的限制，通常只有几百个碱基对。这些“短文”给高质量的微生物基因组重建和复杂微生物群中基因的准确分类带来了挑战，从而阻碍了我们衡量微生物多样性和预测生态系统代谢功能和活动的能力。另一方面，新的单分子DNA测序技术在允许的读取长度上基本上是无限的，并通过显著改进基因的组装和分类来推动基因组学革命。在这里，我们正在申请资金购买一个高通量的单分子测序平台，该平台将为不列颠哥伦比亚大学的微生物组和基因组学研究人员提供新的能力。这种设备将满足迫切的需求，因为目前还没有高通量的单分子长读测序平台向不列颠哥伦比亚大学的研究人员开放。这种设备将通过加强在人类健康、农业、生物地质科学和环境生物技术领域的研究竞争力和影响，直接使加拿大受益。这些设备将在不列颠哥伦比亚大学的一个共享设施中托管和维护，以确保跨越广泛学科的微生物组和基因组学研究人员可以有效和公开地使用它。根据该团队目前的研究活动，以及共享设施中DNA测序仪的当前使用情况，我们预计每年至少有60名HQP将从该设备的培训中受益。总体而言，该设备将确保不列颠哥伦比亚省的研究人员在基因组学领域处于领先地位，并将为HQP提供变革性分子生物技术方面的适销对路和尖端经验。

Microorganisms are `microscopic chemical factories' that underpin planetary and human health. Even though the majority of biological diversity on our planet is held within single-celled microorganisms, our ability to study these microbes is challenged by our inability to culture a vast majority of them in the laboratory. Therefore, the study of microbial communities within in their in situ habitats, or microbiomes, has been bolstered by advances in genomic sequencing technologies over the past several decades. These high-throughput sequencing technologies enable the in situ study of microbiomes through the application of metagenomics, which involves massive sequencing of environmental DNA to reconstruct high-quality microbial genomes, and/or through high-throughput gene amplicon sequencing. Recent discoveries in microbiome science have empowered new theories related to human health, ocean nutrient cycling, and environmental pollution treatment and control. Despite such breakthroughs, conventional DNA sequencing technologies still have a key limitation in their allowable read length, which typically is only a few hundred base-pairs. These `short-reads' create challenges for high-quality microbial genome reconstruction and accurate taxonomic classification of genes in complex microbiomes, thus hindering our ability to measure microbial diversity and predict metabolic function and activity across ecosystems. On the other hand, new single-molecule DNA sequencing technologies are essentially unlimited in their allowable read length, and are driving a genomics revolution by dramatically improving assemblies and taxonomic classification of genes. Here, we are requesting funds to purchase a high-throughput single-molecule sequencing platform that will provide new capabilities to microbiome and genomics researchers at the University of British Columbia. This equipment will fulfill an urgent need, as there is currently no high-throughput single-molecule long-read sequencing platform openly available to researchers at the University of British Columbia. This equipment will directly benefit Canada by strengthening research competitiveness and impact in the fields of human health, agriculture, biogeosciences, and environmental biotechnology. The equipment will be hosted and maintained in a shared facility at the University of British Columbia, ensuring that it can be effectively and openly utilized by microbiome and genomics researchers spanning broad disciplines. Based on the current research activities by the team, and current usage of DNA sequencers at the shared-facility, we expect at least 60 HQP will benefit from training on this equipment annually. Overall, this equipment will ensure that researchers in British Columbia are leaders in genomics, and will provide HQP with marketable and cutting-edge experience in a transformative molecular biotechnology.