Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

Abstract

Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters

“…We sequenced the 14 strains using the Ion Torrent PGM, with 400 bp sequencing libraries and 400 bp sample preparation and sequencing chemistry (Rothberg et al, 2011;Yamanaka et al, 2014). The limitations of using next-generation sequencing, specifically for the discovery of secondary metabolites, are many and varied (Gomez-Escribano et al, 2016). Read length and high G+C content of the DNA are the two biggest hurdles to overcome.…”

Molecular beacons to identify gifted microbes for genome mining

“…The most gifted strains could be targeted for complete genome sequencing, which is now feasible and relatively inexpensive by using a combination of Illumina and PacBio sequencing. 16,[52][53][54] By adding additional CP-TEs from other taxons, the CP-TE multi-probe approach can be adapted to survey draft genomes of other bacteria with large genomes, such as species of the Myxobacteria, Burkholderia and Photorhabdus, all of which have gifted members that encode multiple SMGCs. 16 …”

Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes

“…For example, long-read sequencing technologies, such as the NanoPore Minion and the PacBio SMRT, will help to overcome the challenges currently posed by metagenomic assembly from short-read data, providing greater information about functions encoded in large operons, such as biosynthetic and multidrug-resistance gene clusters. 140,149,150 Furthermore, cheaper sequencing will allow for deeper sequencing, improving our ability to assemble metagenomes and profile antimicrobial resistance and biosynthetic capacities. 83 Single-molecule sequencing, particularly when combined with short-read shotgun metagenomic data, may also improve metagenomic assembly and allow for better identification of biosynthetic gene clusters.…”