Phylogenomic Analysis of Antibiotic Biosynthesis Gene Clusters in Soil Actinomycetes
DOI:
https://doi.org/10.5281/zenodo.22687709Keywords:
biosynthetic gene clusters, actinomycetes, phylogenomics, antibiotic discovery, secondary metabolism, soil metagenomicsAbstract
Soil actinomycetes remain the single richest natural source of clinically used antibiotics, yet the great majority of
the biosynthetic gene clusters (BGCs) encoded in their genomes have never been linked to an isolated
compound, a gap commonly described as cryptic or silent biosynthetic potential. We conducted a systematic
phylogenomic survey of 1,842 publicly available actinomycete genomes spanning 47 genera, identifying and
classifying 21,406 biosynthetic gene clusters with antiSMASH and cross-referencing predicted cluster products
against the MIBiG and NPAtlas reference databases to distinguish clusters with a known product from those that
remain functionally uncharacterised. Sequence similarity networking of clusters encoding non-ribosomal peptide
synthetases and type I polyketide synthases, the two BGC classes responsible for the large majority of clinically
important actinomycete antibiotics, resolved 3,912 gene cluster families, of which only 612 (15.6%) could be
confidently linked to a characterised product, leaving 3,300 families of uncertain biosynthetic output. Mapping
cluster family distribution against a genus-level phylogeny built from 120 conserved marker genes showed that
biosynthetic novelty is not evenly spread: genera isolated primarily from under-sampled soil environments,
including semi-arid grassland and high-altitude alpine soils, harboured a significantly higher proportion of orphan
gene cluster families than genera dominated by temperate agricultural soil isolates, a pattern that held after
controlling for genome assembly quality and sampling depth per genus. A focused case study on eleven orphan
clusters showing strong sequence homology to validated antitumour or antifungal biosynthetic pathways, but
lacking any matched product, is presented as a prioritised shortlist for downstream heterologous expression.
These results indicate that the biosynthetic dark matter of soil actinomycetes remains substantial and
non-randomly distributed across the phylogeny and across sampling environments, and that systematic genome
mining targeted at under-sampled lineages is likely to be a more productive discovery strategy than continued
resequencing of already well-characterised genera.
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