From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology. Issue 6 (June 2018)

• Record Type: Journal Article
• Authors: Nai, Corrado; Meyer, Vera
• Is Part Of: Trends in microbiology. Volume 26:Issue 6(2018)
• Page Start: 538
• Page End: 554
• Publication Date: 2018-06
• Subjects: cocultivation (co-cultivation) devices -- coculture (co-culture) -- microfluidic devices -- natural product discovery -- microbial secondary metabolism -- microbial communication; Microbiology -- Periodicals; Infection -- Periodicals; Virulence (Microbiology) -- Periodicals; Infection -- Periodicals; Microbiology -- Periodicals; Virulence -- Periodicals; Microbiologie -- Périodiques; Infection -- Périodiques; Virulence (Microbiologie) -- Périodiques; Infection; Microbiology; Virulence (Microbiology); 579
• DOI: 10.1016/j.tim.2017.11.004
• Languages: English
• ISSNs: 0966-842X

Abstract

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. Trends: A limited, biased, and anthropocentric view of the microbial world with focus on fast-growingcopiotrophic species has emerged from classical axenic cultivation approaches. Recent (meta)genomic insights unveiled the potential hidden in microbial diversity. However, cultivation-independent approaches cannot replace cultivation techniques. Cultivation techniques have to evolve further – from axenic to mixed cultures – to fully understand the microbial world. Newly emerged tools, including microfluidics, bioprinting, high-throughput screening, and single-cell analytics, need to be fully implemented and integrated with existing (microbiology) techniques to systematically investigate and exploit microbial cocultures.