Advances in actinomycete research: an ActinoBase review of 2019

Abstract

The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.

Keywords: ActinoBase; Actinobacteria; Streptomyces; antibiotics; development; methodology; microbial ecology; regulation; specialized metabolites; symbiosis.

Fig. 1.

The life cycle of filamentous actinomycetes based upon the model organism S. venezuelae . Development begins with the formation of one or two germ tubes from a spore. Following germination, mycelial outgrowth leads to the formation of vegetative mycelium. Transition from vegetative growth to aerial hyphae production occurs upon detection of signals, e.g. nutrient depletion. The aerial hyphae septate and mature into chains of pigmented spores that disperse, and the cycle can then begin again.

Fig. 2.

Graphic showing the general antibiotic compound discovery pipeline. The process usually begins with the isolation of novel strains or DNA from environmental samples. Once genomes and metagenomes are sequenced and assembled, the sequences can be analysed with tools such as RiPPER, antiSMASH or ARTS to identify biosynthetic gene clusters (BGCs). A combination of cluster synthesis, cloning and heterologous expression, or strain manipulation through CRISPR or varied conditions, can then be used to encourage the production of novel antibiotics. The production of antibiotics is screened for using bioactivity assays. Compounds can then be further characterized using techniques such as NMR or mass spectrometry.