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.

微生物是基础行星和人类健康的“微观化学工厂”。尽管我们星球上的大多数生物多样性都在单细胞微生物中举行，但我们研究这些微生物的能力受到我们无法在实验室中培养绝大多数的培养它们的挑战。因此，在过去的几十年中，基因组测序技术的进步增强了对其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可以通过应用元基因组学对微生物组进行原位研究，元基因组学涉及将环境DNA进行大规模测序以重建高质量的微生物基因组和/或通过高关注的高量基因组基因测序。微生物组科学的最新发现赋予了与人类健康，海洋营养循环以及环境污染治疗和控制有关的新理论。 尽管有这样的突破，但常规的DNA测序技术在其允许的读取长度上仍然具有关键的限制，通常只有几百个碱基对。这些“短阅读”对复杂微生物组中基因的高质量微生物基因组重建和准确的分类分类构成了挑战，从而阻碍了我们测量微生物多样性并预测生态系统中的代谢功能和活性的能力。另一方面，新的单分子DNA测序技术在允许的读取长度中基本上是无限的，并且正在通过大大改善基因的组件和分类分类来推动基因组革命。在这里，我们要求资金购买高通量单分子测序平台，该平台将为不列颠哥伦比亚大学的微生物组和基因组研究人员提供新的功能。该设备将满足迫切的需求，因为目前没有不列颠哥伦比亚大学的研究人员公开使用的高通量单分子长读测序平台。该设备将通过增强研究竞争力和对人类健康，农业，生物科学和环境生物技术领域的影响而直接受益。该设备将在不列颠哥伦比亚省大学的共享设施中托管和维护，以确保微生物组和基因组学研究人员可以有效并公开利用它。根据团队当前的研究活动以及当前在共享功能上使用的DNA测序仪的使用，我们预计每年至少有60个HQP将受益于该设备的培训。总体而言，该设备将确保不列颠哥伦比亚省的研究人员是基因组学领域的领导者，并将在变革性分子生物技术中为HQP提供可销售和尖端的经验。