Establishment of an innovative co-cultivation platform for high-throughput identification of antimicrobial compounds

在多重耐药致病菌和真菌反复出现的令人担忧的背景下，必须探索微生物学研究和生物工艺工程的未知领域。培养纯（无菌）微生物的流行方法，自19世纪末由罗伯特·科赫（Robert Koch）引入至今仍然是普遍的做法，必须采用创新技术来建立混合物种培养。在过去的二十年中，为了寻找新的抗生素和抗真菌基因，对丝状真菌和细菌的基因组序列数据进行了深入的研究，结果出人意料地发现，在大多数测序的物种中，大约存在30-50个基因簇，这与从真菌青霉菌中发现的青霉素类似，可能会开启一个新的医学时代。令人惊讶的是：当细菌和真菌在无菌培养基中培养时，大多数发现的基因簇是无活性的，不会导致生物活性物质的产生。因此，传统微生物学研究方法无法充分利用这种潜力，这也是近20年来无法从微生物纯培养物中鉴定出新型抗生素的关键原因之一。低垂的果实已经收获，单一物种种植的时代必须结束。通过考虑混合种培养物的代谢活动，包括分析无法作为纯培养物存活的不可培养微生物的代谢，可以实现科学突破。这种分析必须在系统生物学水平（转录组学、蛋白质组学和代谢组学）上进行，以便对微生物代谢进行从基因型到化学型的全面了解，并为可控制和可重复的培养方法提供新的技术方法，以确保产生可靠和稳健的数据。本提案的研究概念符合开发新的共同培养方法和方法的要求，以便在体外稳定培养天然的、复杂的混合物种微生物种群，发现迄今未知的物质和物质类别，以应对当前的社会和医疗挑战，测试它们作为抗菌和抗真菌的生物活性，以及与相应遗传簇的相关性。

In the alarming context of the recurrent emergence of multi-resistant pathogenic bacteria and fungi, uncharted territories in microbiological research and bioprocess engineering must be explored. The prevailing method of growing pure (axenic) culture of microorganisms, as of today still the common praxis since its introduction by Robert Koch in the late XIX century, must be implemented with innovative technologies for the establishment of mixed-species cultures.The intensive investigation during the last two decades of genome sequence data from filamentous fungi and bacteria in the quest for new antibiotic and antimycotic genes led to the unexpected observation that in most sequenced species about 30-50 gene clusters are present, which similarly to penicillin from the fungus Penicillium chrysogenum could set in motion a new era in medicine. The surprise: most of the discovered gene clusters are inactive and do not lead to the production of a bioactive substance when bacteria and fungi are cultivated in axenic cultures. This potential cannot thus be fully exploited with methodologies used in classical microbiological studies and is one of the pivotal reasons why since about 20 years no new class of antibiotic could be identified from microbial pure cultures. The low-hanging fruits have been harvested and the end of the era of single-species cultivations muss be ushered. Scientific breakthroughs can be achieved by considering the metabolic activities of mixed-species cultures including the analysis of the metabolism of yetuncultivable microorganisms that are not viable as pure cultures. This analysis must occur at the systems biology level (transcriptomic, proteomic and metabolomics) to allow for a holistic, from genotype-to-chemotype understanding of microbial metabolism as well as to provide new technical approaches for a controlled and reproducible cultivation methodology to ensure the generation of reliable and robust data.The research concept of the present proposal meets the requirements for the development of new co-cultivation approaches and methodologies for the stable in vitro cultivation of natural, complex mixed-species populations of microorganisms for the discovery of hitherto unknown substances and substance classes for current societal and medical challenges, their bioactivity testing as antibacterials and antifungals as well as the correlation with the corresponding genetic clusters.