Platform for the automated isolation and characterization of anaerobic bacteria

• Subject Area: Medicine
• Term: Funded in 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 445552570

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”).

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Plattform zur automatisierten Isolierung und Charakterisierung von anaeroben Bakterien
• Instrumentation Group: 1060 Dilutoren, Pipettiergeräte, Probennehmer
• Applicant Institution: Rheinisch-Westfälische Technische Hochschule Aachen
• Leader: Professor Dr. Thomas Clavel