Back to soil: Awakening the production of cryptic antibiotics in Streptomyces

Most of the antibiotic biosynthetic gene clusters (BGCs) in Streptomyces are not expressed under laboratory conditions, however these clusters are maintained in the genomes, therefore indicating that they must play important roles in adaptation and survival within their ecological niches. Understanding the global regulation patterns that affect transcription of antibiotic BGCs in soil conditions versus laboratory conditions allows us to identify novel routes for up- or down- regulation in order to trigger expression of these BGCs and therefore production of these antibiotics under controlled laboratory and fermentation conditions. Cryptic pathways represent an untapped resource in terms of new metabolites that could be very useful in the clinic if we can awaken their expression and production. We are using RNA sequencing to analyse global transcriptional patterns of S. venezuelae and S. rimosus grown in sterile soil, non-sterile soil and standard laboratory solid medium, as well as using an unbiased metabolomics approach to identify compounds produced in soils. These results will enable the identification of global regulatory pathways that activate cryptic clusters in nature and lead to the production of these compounds in soil. This will enable us to generate genetically modified strains engineered to increase the yield of both well characterised and cryptic clusters which encode potentially novel compounds under industrial fermentation conditions. It is worth noting that the transcriptional data may also help shed light on the complex regulation of the life cycle of these Streptomyces strains in an ecologically relevant environment

Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21

Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions

Mesoscale standing wave imaging

Standing wave (SW) microscopy is a method that uses an interference pattern to excite fluorescence from labelled cellular structures and produces high-resolution images of three-dimensional objects in a two-dimensional dataset. SW microscopy is performed with high-magnification, high-numerical aperture objective lenses, and while this results in high-resolution images, the field of view is very small. Here we report upscaling of this interference imaging method from the microscale to the mesoscale using the Mesolens, which has the unusual combination of a low-magnification and high-numerical aperture. With this method, we produce SW images within a field of view of 4.4 mm × 3.0 mm that can readily accommodate over 16,000 cells in a single dataset. We demonstrate the method using both single-wavelength excitation and the multi-wavelength SW method TartanSW. We show application of the method for imaging of fixed and living cells specimens, with the first application of SW imaging to study cells under flow conditions

Mesoscale standing wave imaging

Standing wave (SW) microscopy is a method that uses an interference pattern to excite fluorescence from labelled cellular structures and produces high-resolution images of three-dimensional objects in a two-dimensional dataset. SW microscopy is performed with high magnification, high numerical aperture objective lenses, and while this results in high resolution images, the field of view is very small. Here we report upscaling of this interference imaging method from the microscale to the mesoscale using the Mesolens, which has the unusual combination of a low magnification and high numerical aperture. With this method, we produce SW images within a field of view of 4.4 mm x 3.0 mm that can readily accommodate over 16,000 cells in a single dataset. We demonstrate the method using both single-wavelength excitation and the multi-wavelength SW method TartanSW. We show application of the method for imaging of fixed and living cells specimens, with the first application of SW imaging to study cells under flow conditions