From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology

Abstract

Since the onset of microbiology in the late 19th century, scientists have been growing microorganisms almost exclusively as pure cultures, resulting in a limited and biased view of the microbial world. Only a paradigm shift in cultivation techniques - from axenic to mixed cultures - can allow a full comprehension of the (chemical) communication of microorganisms, with profound consequences for natural product discovery, microbial ecology, symbiosis, and pathogenesis, to name a few areas. Three main technical advances during the last decade are fueling the realization of this revolution in microbiology: microfluidics, next-generation 3D-bioprinting, and single-cell metabolomics. These technological advances can be implemented for large-scale, systematic cocultivation studies involving three or more microorganisms. In this review, we present recent trends in microbiology tools and discuss how these can be employed to decode the chemical language that microorganisms use to communicate.

Thinking Outside the Box—Novel Antibacterials To Tackle the Resistance Crisis

“…This identification strategy has become well-known as the Waksman platform, in honor of the pioneering work of Nobel laureate Selman Waksman. [24] Since microbes concomitantly faced optimal growth conditions (e.g.excess of nutrients,constant temperature,and pH value), they were not triggered to produce all the secondary metabolites they would use in an atural environment to interact with nearby organisms.Several authors have reviewed potential methods to induce the expression of the silent biosynthetic gene clusters (BGCs) of these metabolites, for example,b yv arying the cultivation conditions or by genomic engineering. However,o ver the last few decades,t raditional natural product extract screenings failed to unravel new active antibiotics.I np articular,t he rediscovery of already known natural products has become asignificantly hurdle which has dramatically increased the attrition rates of natural product discovery.…”

“…[17] Form any years, Actinomycetes were the most important resource in terms of number and diversity of natural products. [23][24][25][26] Thec ocultivation of multiple bacterial species has proven to be very effective for the production of previously unknown secondary metabolites ( Figure 2a). [22] As the "low-hanging fruits" of antibiotic natural products have already been picked, novel approaches are urgently needed.…”

“…However,o ver the last few decades,t raditional natural product extract screenings failed to unravel new active antibiotics.I np articular,t he rediscovery of already known natural products has become asignificantly hurdle which has dramatically increased the attrition rates of natural product discovery. [24,27,28] Ar ecent successful example is the coculturing of two marine species,t he producer Micromonospora together with Rhodococcus sp., to afford the bis-nitroglycosylated anthracycline keyicin ( Figure 3). Thea daptation of laboratory cultivation methods was shown to be an effective strategy to revive natural product discovery.I na ll natural environments (such as soil, plants,orthe human gut), microbes live in association with am ultitude of other organisms and interact with these through antagonism, commensalism, or mutualism.…”

Beyond the biosynthetic gene cluster paradigm: Genome-wide co-expression networks connect clustered and unclustered transcription factors to secondary metabolic pathways

“…Thus, wholesale modulation of fungal SMs in standard lab culture is possible using hypotheses derived from both Spearman/mutual rank network approaches. The simplicity of the culture conditions is an attractive aspect of the discovery pipeline in this work, which may be preferable when compared to more complex experimental setups, such as co-cultivation experiments, or isolation of novel metabolites from the complex fungal niche (e.g., soil) or marine environments 57 .…”

Über bisherige Denkweisen hinaus – neue Wirkstoffe zur Überwindung der Antibiotika‐Krise

“…[21] Tr aditionell werden fürd ie Entdeckung von potentiell bioaktiven Naturstoffkandidaten Mikroorganismen kultiviert und ihre Metaboliten auf einen phänotypischen Effekt hin untersucht. [24] Da die Mikroorganismen zusätzlich optimale Wachstumsbedingungen vorfan-wachsen würden. In Anerkennung der wegweisenden Arbeiten des Nobelpreisträgers Selman Waksman bezeichnet man diese Strategie auch als die Waksman-Plattform.…”