Platform for the automated isolation and characterization of anaerobic bacteria

人体上/体内的微生物组在健康中起着重要作用，但也与慢性疾病如炎症和代谢性疾病的发作有关。因此，评估其多样性和功能至关重要。一个很大的障碍是，超过50%的微生物群成员仍然未知。因此，微生物的培养非常重要，因为它允许描述新的多样性并进行下游机制研究。然而，培养工作由于肠道中许多微生物的厌氧需求而变得复杂。经典的厌氧技术起源于20世纪60年代，迫切需要开发创新的方法。申请的平台解决了这个问题。其目标是高通量分离、培养、鉴定、表征和储存厌氧菌。它基于单细胞分选和培养物的自动化处理。在本申请中，主要目标生态系统是哺乳动物肠道，但该平台也可以应用于其他生态系统。尽管经过15年的测序研究和许多团体对分离细菌的兴趣之后，培养复兴，但该平台在同类产品中是尖端和独特的，并依赖于宿主实验室多年的厌氧培养经验。该平台的一个主要资产是能够创建个性化的、宿主特异性的分离物目录，考虑到肠道微生物组的菌株特异性和宿主特异性，这一点非常重要。它将大大有助于探索个性化的干预策略，在实验和临床研究中有针对性地使用简化的培养微生物群落，即所谓的生物治疗。因此，它将为微生物生态学和生物医学的创新研究开辟道路，并将为国内机构的多个DFG资助的研究联盟（CRC 1382“肠道-肝脏轴”; SFB/TRR 219“慢性肾脏疾病”; CRU 344“骨髓增生性肿瘤”）和其他国家倡议（例如CRC 1371“微生物组特征”）服务。

Microbiomes on/in the human body play an important role in health but have also been implicated in the onset of chronic disorders such as inflammatory and metabolic diseases. Hence, it is crucial to assess their diversity and functions. A big obstacle is that >50% of microbiota members are still unknown. The cultivation of microbes is thus very important, as it allows describing novel diversity and performing downstream mechanistic studies. However, culture work is complicated by the anaerobic requirement of many microbes in the gut. Classical anaerobic techniques originate from the 1960’s and there is urgent need to develop innovative approaches.The platform applied for tackles this issue. Its goal is high-throughput isolation, cultivation, identification, characterization, and storage of anaerobic bacteria. It is based on single-cell sorting and automatized handling of cultures. In the present application, the main target ecosystem is the mammalian gut, but the platform can be applied to other ecosystems too. Despite both the renaissance of cultivation after 15 years of research dominated by sequencing and the interest of many groups to isolate bacteria, the platform is cutting-edge and unique in its kind and relies on years of experience in anaerobic cultivation in the host lab. A major asset of the platform is the ability to create individualized, host-specific catalogues of isolates, which is very important considering both the strain- and host-specificity of gut microbiomes. It will substantially help exploring individualized intervention strategies towards targeted use of simplified communities of cultured microbes, so called biotherapeutics, in both experimental and clinical research. It will thus open avenues to innovative research in microbial ecology and biomedicine and will serve the purpose of multiple DFG-funded research consortia at the home institution (CRC1382 “Gut-liver axis”; SFB/TRR219 “Chronic Kidney Disease”; CRU344 “Myeloproliferative neoplasms”) and other national initiatives (e.g. CRC1371 “Microbiome signatures”).