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

在多重耐药病原菌和真菌不断出现的令人震惊的背景下，必须探索微生物学研究和生物过程工程方面的未知领域。目前流行的纯(无菌)微生物培养方法，自罗伯特·科赫在十九世纪末引入以来仍然是常见的方法，必须利用创新技术来建立混合菌种培养。在过去二十年中，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，结果意外地观察到，在大多数测序物种中，大约存在30-50个基因簇，这类似于来自真菌产黄青霉的青霉素，可能会开启医学的一个新时代。令人惊讶的是：当细菌和真菌在无菌培养中培养时，大多数发现的基因簇都是不活跃的，不会导致生物活性物质的产生。因此，这一潜力不能用经典微生物学研究中使用的方法来充分开发，这是自大约20年来从微生物纯培养物中找不出新的抗生素类别的关键原因之一。低垂的果实已经收获，单一品种栽培的时代即将结束。科学突破可以通过考虑混合菌种培养的代谢活动来实现，包括分析尚未培养的微生物的代谢，这些微生物作为纯培养物是不可行的。这种分析必须在系统生物学(转录学、蛋白质组学和代谢组学)的水平上进行，以实现对微生物代谢的全面、从基因到化学类型的了解，并为受控和可重现的培养方法提供新的技术途径，以确保产生可靠和稳健的数据。本提案的研究概念满足开发新的共培养途径和方法的要求，用于稳定体外培养自然、复杂的混合物种微生物种群，以发现迄今未知的物质和物质类别，以应对当前的社会和医学挑战，作为抗菌剂和抗真菌药物的生物活性测试以及与相应基因簇的相关性。

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.