High-throughput nanoscale culture and screening applications for microbiome research

未培植的微生物代表了地球上看不见的大多数生物。据估计，地球上有10^30种原核生物微生物，包括三个领域中的两个，并辐射到许多没有培养代表的“暗物质”部门。微生物的丰度超过了已知宇宙中恒星的数量、我们大脑中神经元的数量以及我们所有突触的总和。相互关联的微生物群落共同推动物质和能量转换过程，帮助创造和维持地球上生命的条件。35亿多年来，微生物一直在进化，以解决个人、种群和社区层面的复杂新陈代谢问题，为养分和能量转换过程创新了分布式解决方案，这些解决方案经受住了时间的考验，并产生了深层次的基因组潜力。这种潜力包括无数的新陈代谢过程以及适应当地环境条件的酶变体。为了获得这个微观世界隐藏的新陈代谢问题解决能力，我们需要新的平台和方法来提供一致的分类解决方案、封闭的参考基因组和潜在的遗传可控性。当与功能筛选相结合以发现新的酶功能时，我们将准备超越已知的代谢相互作用的图谱，进入对生物系统的更深层次的理解。在这里，我们建议结合高通量纳米级培养和筛选应用程序，利用名为Prospector的变革性自动化系统的能力来分离参与厌氧消化、尾矿修复和木质纤维素生物质转化的关键微生物。由此产生的分离物收集将用于生成用于代谢途径推断的封闭参考基因组，并在与平板和微流控液滴形式的功能筛选应用相结合时，使合成微生物联合体和全细胞生物催化剂的开发成为可能。Prospector的使用将有助于培训一支多元化和跨学科的高素质人员队伍，在生命科学和工程学的多个研究小组和院系工作，并为代谢途径工程和跨部门生物技术创新开辟新的机会，以支持加拿大新兴的生物经济。

Uncultivated microorganisms represent the invisible majority of living things on Earth. There are an estimated 10^30 prokaryotic microorganisms on the planet, encompassing two of three domains and radiating into numerous “dark matter” divisions with no cultured representatives. Microbial abundance eclipses the number of stars in the known universe, the number of neurons in our brains and all of our synapses combined. Collectively, interconnected microbial communties drive matter and energy conversion processes that help create and sustain the conditions for life on Earth. For over 3.5 billion years microorganisms have evolved to solve complex metabolic problems at the individual, population and community levels, innovating distributed solutions to nutrient and energy conversion processes that have withstood the test of time and generated a deep reservoir of genomic potential. This potential includes countless metabolic processes as well as enzyme variants adapted to local environmental conditions. In order to access the hidden metabolic problem-solving power of this microcosmos we need new platforms and approaches that provide coherent taxonomic resolution, closed reference genomes and the potential for genetic tractability. When combined with functional screening to uncover novel enzyme functions we become poised to move beyond the known cartography of metabolic interactions into a deeper understanding of biological systems. Here we propose to combine high-throughput nanoscale culture and screening applications leveraging the capabilities of a transformative automation system called the Prospector to isolate key microbial players involved in anaerobic digestion, mine tailings remediation and lignocellulose biomass conversion. Resulting isolate collections will be used to generate closed reference genomes for metabolic pathway inference and enable the development of synthetic microbial consortia and whole-cell biocatalysts when combined with functional screening applications in both plate-based and microfluidic droplet formats. Use of the Prospector will contribute to the training of a diverse and interdisciplinary cadre of highly qualified personnel working across multiple research groups and faculties in the Life Sciences and Engineering and open up new opportunities for metabolic pathway engineering and cross-sector biotechnology innovation in support of the emerging bioeconomy in Canada.