A pipeline for high-throughput microbial isolation, sorting, screening and synthetic community assembly

微生物作为不同物种（如细菌和真菌）的复杂群落生活，在植物和动物的健康和疾病中发挥关键作用，支持全球营养循环，并代表可用于解决医学，农业和工业中重大社会挑战的多种代谢途径和酶的来源。由于微生物群落的复杂性，可以包含数以百万计的细胞和数以千计的微生物个体，分离出单个细胞，在实验室中作为纯培养物生长和研究它们，对它们的基因组进行测序，了解它们的生理，或筛选它们的新酶和发现新的微生物化合物（例如抗生素）是一个巨大的挑战。然而，现在新兴的先进技术使这成为可能，这些技术可以将单个细胞分离成微液滴，并选择或分类液滴以进行进一步的实验室分析。在这里，我们将结合三台设备来开发一个实验管道，这将使我们能够从复杂的群落（或细胞群体）中分离单个微生物细胞，并将它们封装在水/油或凝胶液滴中，然后可以对数百万液滴进行分类和选择以进行进一步筛选。这种方法使用了目前尚未广泛使用的新的先进研究技术，将显著提高数百万细胞/液滴的分析速度。该设备将面向广泛的用户群体，并将支持快速和重大的研究进展，这将推动我们将微生物分离到纯培养中，研究其生物学，并发现新的酶和微生物化合物的能力的逐步变化，这些酶和微生物化合物可以解决与植物和人类健康，微生物功能，酶发现，抗菌素耐药性筛选，发现新的抗菌素化合物，废物管理和可持续能源生产。

Microorganisms live as complex communities of different species (e.g. of bacteria and fungi) and play key roles in health and disease in plants and animals, support global nutrient cycles, and represent a source of diverse metabolic pathways and enzymes that can be used to address grand societal challenges in medicine, agriculture and industry. Due to the complexity of microbial communities that can contain millions of cells and thousands of individual species of microbe, separating out individual cells to grow and study them as pure cultures in the laboratory, sequence their genome, understand their physiology, or to screen them for new enzymes and discover new microbial compounds (e.g. antibiotics) is a huge challenge. However, this is now made possible by emerging advanced technologies that separate single cells into microdroplets and select or sort droplets for further laboratory analysis. Here, we will combine three pieces of equipment to develop an experimental pipeline that will enable us to separate single microbial cells from a complex community (or population of cells) and encapsulate them in water/oil or gel droplets where millions of droplets can then be sorted and selected for further screening. This approach uses new advanced research technology that is currently not widely available and will significantly increase the speed at which millions of cells/droplets can be analysed. The equipment will be accessible to a broad user community and will support rapid and significant research advances that will drive a step-change in our ability to isolate microbes into pure culture, to study their biology, and discover new enzymes and microbial compounds that can address grand challenges relating to plant and human health, microbial function, enzyme discovery, screening for antimicrobial resistance, discovery of new antimicrobial compounds, waste management and sustainable energy generation.