Advancing microbiome science with long-read sequencing

通过长读长测序推进微生物组科学

• 批准号: RTI-2023-00352
• 负责人: Ziels, Ryan
• 金额: $ 9.78万
• 依托单位: University of British Columbia
• 依托单位国家: 加拿大
• 项目类别: Research Tools and Instruments
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=749455
• 关键词: Advancing; microbiome; science; long; read

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.

微生物是支撑地球和人类健康的“微观化学工厂”。尽管我们星球上的大多数生物多样性都存在于单细胞微生物中，但我们研究这些微生物的能力受到了挑战，因为我们无法在实验室中培养绝大多数微生物。因此，在过去的几十年里，基因组测序技术的进步促进了对原位栖息地或微生物组中微生物群落的研究。这些高通量测序技术使得能够通过应用宏基因组学对微生物组进行原位研究，宏基因组学涉及对环境DNA进行大规模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为人类健康、海洋营养循环和环境污染处理和控制提供了新的理论。 尽管有这样的突破，常规DNA测序技术在其允许的读取长度方面仍然具有关键限制，其通常仅为几百个碱基对。这些“短读数”给高质量的微生物基因组重建和复杂微生物组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整个生态系统代谢功能和活动的能力。另一方面，新的单分子DNA测序技术在其允许的读取长度上基本上是无限的，并且通过显著改善基因的组装和分类学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单分子测序平台，该平台将为不列颠哥伦比亚省大学的微生物组和基因组学研究人员提供新的能力。该设备将满足迫切的需求，因为目前没有高通量单分子长读段测序平台可供不列颠哥伦比亚省大学的研究人员公开使用。这些设备将通过加强研究竞争力和在人类健康、农业、生物科学和环境生物技术领域的影响，使加拿大直接受益。这些设备将在不列颠哥伦比亚省的一个共享设施中托管和维护，以确保跨学科的微生物组和基因组学研究人员能够有效和公开地利用这些设备。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。总的来说，这些设备将确保不列颠哥伦比亚省的研究人员成为基因组学的领导者，并将为HQP提供变革性分子生物技术方面的市场和尖端经验。