Accelerating novel antibiotic discovery: Actinomycetes and actinophages
Health & Medicine
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The discovery of penicillin from a fungus was a major breakthrough in the field of medicine. It has since saved countless lives from bacterial infections. However, the ready availability of antibiotics, coupled with their injudicious use, has resulted in the emergence of multidrug-resistant (MDR) pathogens. MDR organisms pose a significant threat to our healthcare systems, creating a need for novel and potent anti-microbial formulations. Dr İpek Kurtböke, Associate Professor at the University of the Sunshine Coast (USC), Australia, has been actively contributing solutions to this issue through her relentless efforts in the biodiscovery of antibiotics from novel sources, such as actinomycetes, a type of bacteria. Dr Kurtböke and her team are currently investigating the metabolic pathways of members of actinomycetes to determine their biosynthetic potentials. They also use actinophages (viruses that infect these bacteria) as tools to aid selective recovery of rare actinomycete species.
The first major breakthrough in the world of antibiotics was the discovery of penicillin in 1928. Since then, microbial species have been a key topic of research. Penicillin led to the development of a widely accessible treatment of bacterial infections, which significantly reduced mortality rates in patients. It is made from a type of mould called Penicillium – a genus of ascomycetous fungi. The discovery of a second potent antibiotic called streptomycin, synthesised by the bacterium Streptomyces griseus, ushered in the first ‘Golden era’ of antibiotics (1940–1974). Since then, actinomycetes (a group of gram-positive bacteria with filamentous structures) have accounted for almost 45% of bioactive secondary metabolites discovered so far.
Key antibiotics sourced from the Streptomyces genus include kanamycin, neomycin, gentamicin, and vancomycin. In addition, a predictive modelling theory proffered by Watve et al (2001) suggested that natural antibiotic reserves are far from exhausted. He stated that there could be over 150,000 bioactive metabolites still waiting to be discovered from the members of the genus Streptomyces alone. Previous research by Baltz (2005) also noted that antibiotic biosynthetic pathways are still going through the evolutionary process. Moreover, recent genomic advances – such as genome mapping, next-generation sequencing, rRNA sequencing, metagenomics, and data mining – could lead to a greater understanding of rarer compounds waiting to be discovered from actinomycetes.
Internationally renowned actinomycetologist Dr İpek Kurtböke at the University of the Sunshine Coast, Australia, is looking at microbial genomes, and has outlined silent genes and cryptic pathways in actinomycetes, especially from the rare ones. Kurtböke started investigating actinomycetes in 1982 during the second golden era of antibiotics (1975–2000) and remains a key researcher in the field of biodiscovery today. Kurtböke’s polyphasic analyses of actinomycete communities has bolstered the available dataset for screening diverse actinomycetes and their novel bioactive compound synthesis needed for future research. Here, we look at some of the methods and implications of her research.
Streptomyces phage. (Kurtböke personal collection)
Unearthing rare bioactive compounds
Tracing diversity and distribution of actinomycetes using bacteriophages (viruses that infect bacteria) as tools was an important development in the second golden era of actinomycetes. To date, Kurtböke’s use of bacteriophages as eco-taxonomic indicators for identifying various underrepresented species has unearthed previously unknown actinomycetes.
“Actinomycetes still remain an unexhausted resource, especially the ones from marine and extreme environments.”
Kurtböke and her team target rare actinomycetes and their metabolites as they produce ‘most diverse, unique, unprecedented, and occasionally complicated compounds with excellent antibacterial potency and usually low toxicity’. Several chemical types such as simple terpenoids or benzenoids are almost completely absent from these compounds. Vancomycin-ristocetin type complicated glycopeptides are produced exclusively by various rare actinomycete species (Berdy, 2005; Baltz, 2005). Currently, only 2,500 bioactive compounds secreted by 50 rare actinomycetes are available.
Kurtböke’s team thus work to develop an extract library obtained from rare actinomycetes with low levels of toxicity and higher antimicrobial potency (ie, the ability to kill or inhibit the growth of bacteria).
Nocardia isolates from sea foam. (İpek Kurtböke, personal collection)
Advancing antibiotic discovery through actinomycetes
Actinomycetes still remain an unexhausted resource, especially the ones from marine and extreme environments. Their untapped potential can be exploited by using a mix of cutting-edge genomics and advance chemical analysis. Techniques such as the use of HSQC-TOCSY Fingerprinting-Directed Discovery approach by Dr Kurtböke’s collaboration with the Griffith Institute of Drug Discovery led to the discovery of Antiplasmodial Polyketides from a Marine Ascidian-Derived Streptomyces sp. (USC-16018) (Buedenbender, et al, 2016, 2017, 2018a, 2018b, 2019) as well as six new natural products from termite gut associated actinomycete (USC-592) using NMR fingerprints (Romero et al., 2015). Such unique approaches would help in the biodiscovery of novel, bioactive compounds, as well as secondary metabolites to aid in the development of natural, sustainable, and low-toxic antibiotics.
Information on a diverse range of genes and proteins can be used for whole-genome sequence mining to discover cryptic or biosynthetic pathways for novel primary and secondary metabolite discovery. Dr Kurtböke’s team thus uses these new-age, advanced genomic techniques on environmental samples isolated from soil and marine ecosystems to reveal the biosynthetic potential of actinomycete resources which might offer diverse bioactive or industrially useful compounds.
An example Nocardia species from foaming coastal marine waters of the Sunshine Coast (Kurtböke, personal collection, images were captured at Central Analytical Research Facility (CARF) at the Queensland University of Technology (QUT), a Microscopy Australia linked lab, 2012), mdpi.com/2076-0817/10/5/579.A bioactive Streptomyces species (USC-633) from near-shore marine environment (Kurtböke, personal collection, images were captured at Central Analytical Research Facility (CARF) at the Queensland University of Technology (QUT), a Microscopy Australia linked lab, 2012), sciencedirect.com/science/article/pii/S2405805X16300424.
Actinophages
Using genus and species-specific phages adds a filtering process to these research endeavours, facilitating the judicious selection of known and novel compounds, and the deselection of known or commonly researched compounds. With antibiotic resistance on the rise, the development of new antibiotics would be a significant boon to medicine for treating difficult microbial infections.
Actinophages specific to family, genera, or species are also used by Dr Kurtböke’s team to uncover hidden natural gems. One example of a polyvalent phage being used to detect bioactive clusters is for the suborders Corynebacterineae, Micromonosporineae, and Pseudonocardineae of actinomycetes. Narrow-spectrum phages, or monovalent phages specific to one genus or species, were also utilised to help to selectively filter clusters of common species that are widely studied, such as the ‘albus, diastaticus and griseus’. They can also aid with the investigation of intra-taxa and intra-species boundaries and the selection of novel and deselection of unwanted actinomycete species. Actinophages have been highly useful for removing unwanted taxa on isolation plates, when rare and bioactive actinomycete isolations are targeted and can also be used to determine taxonomic relatedness of actinomycetes as well as indicating the locations of rare actinomycetes in the environment.
What inspired you to conduct this research?
My first graduate employment involved large-scale production of antibiotic gentamicin produced by an actinomycete. I was fascinated by the beauty and metabolic power of these organisms, and they constructed my career path.
References
Buedenbender, L, Carroll, AR, Kurtböke, Dİ, (2019) Integrated approaches for marine actinomycete biodiscovery. In Frontiers in Clinical Drug Research-Anti Infectives, 5, 1–40. Bentham Science Publishers Ltd.
Buedenbender, L, Carroll, AR, Kurtböke, Dİ, (2019) Detecting co-cultivation induced chemical diversity via 2D NMR fingerprints. Microbiology Australia, 40(4), 186–189.
Buedenbender, L, et al, (2018a) HSQC-TOCSY fingerprinting-directed discovery of antiplasmodial polyketides from the marine ascidian-derived Streptomyces sp. (USC-16018). Marine Drugs, 16(6), 189.
Buedenbender, L, et al, (2018b) HSQC–TOCSY Fingerprinting for prioritization of polyketide-and peptide-producing microbial isolates. Journal of Natural Products, 81(4), 957–965.
Buedenbender, L, et al, (2017) Taxonomic and metabolite diversity of actinomycetes associated with three Australian ascidians. Diversity, 9(4), 53.
Romero, CA, et al, (2015) NMR fingerprints, an integrated approach to uncover the unique components of the drug-like natural product metabolome of termite gut-associated Streptomyces species. RSC Advances, 5(126), 104524–104534.
Dr İpek Kurtböke and her team research actinomycete bioactive compounds for drug discovery. They also use actinophages to selectively recover rare bioactive actinomycetes.
Funding
Brisbane City Council
Terragen Biotech Pty Ltd.
Horticulture Innovation, Australia
Grain Research and Development Cooperation
Australian Research Council
National Landcare Program Innovation Grant
Australian Biological Resources Study
CSIRO
Dept of Agriculture, Fisheries and Forestry (Queensland)
Australian Institute of Marine Science
Collaborators
Brisbane City Council
Research Institute for Marine Fisheries, Hai Phong, Vietnam
Dept of Agriculture and Fisheries, Queensland Government
CSIRO
Terragen Biotech Pty Ltd
Australian Institute of Marine Science
Griffith Institute of Drug Discovery at Griffith University, Australia
