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Volume 9, Issue 4

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using BGC Open Access

Abstract

Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed ineage pecific nalysis of BGCs (BGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. BGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in is ubiquitous across the genus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated . Further, the latter GCF, which is well conserved in , has been lost in most , which is the most common species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the sp. complex, a narrow, multi-species clade that features the most prevalent in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, BGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, BGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bioinformatics , biosynthetic gene clusters , metagenomic mining , microbial evolution , skin microbiome and staphyloxanthin
Funding
This study was supported by the:
  • National Institute of Allergy and Infectious Diseases (Award U19AI142720)
    • Principle Award Recipient: R. KalanLindsay
  • National Institute of General Medical Sciences (Award R35GM137828)
    • Principle Award Recipient: R. KalanLindsay
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-04-25
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Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC
M Gen 9, 000988 (2023); https://doi.org/10.1099/mgen.0.000988
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