Authors
Bing Qian Du, Zi Yu Song, Yu Ting Duan, Yu Tong Kang, Min Yuan, Shuai Xu, Zhen Jun Li
Published in
Biomedical and environmental sciences : BES. Volume 39. Issue 10. Pages 1189-1199. Oct 20, 2026.
Abstract
This study aimed to comprehensively characterize the genomic diversity, evolutionary dynamics, pathogenic potential, antimicrobial resistance, and secondary metabolite capacity of the Nocardia genus using whole-genome analyses.
We analyzed 751 publicly available Nocardia genomes using genome-based species delineation, phylogenomics, pangenome analysis, and comparative functional profiling to assess taxonomy, virulence, antibiotic resistance genes (ARGs), and biosynthetic gene clusters (BGCs).
Phylogenomic analyses resolved five major clades: N. farcinica, N. carnea, N. asteroides, N. transvalensis, and N. otitidiscaviarum groups. The pangenome is open, comprising 467,566 gene clusters and reflecting extensive genomic diversity. Virulence factors and ARGs exhibit clade-specific patterns: the N. farcinica group harbors the most complete virulence repertoire and diverse resistance determinants, whereas the N. carnea and N. asteroides groups carry fewer genes. Analysis of 10,196 BGCs across 46 classes revealed conserved clusters of non-ribosomal peptide synthetases, terpenes, and type I polyketide synthases, with higher biosynthetic potential in the N. farcinica, N. transvalensis, and N. otitidiscaviarum groups. Several genomes encode BGCs associated with antibacterial or anticancer compounds.
This comprehensive genome analysis of Nocardia, representing the most complete sampling to date, clarifies phylogeny, reclassifies misassigned strains, identifies potential novel species, and reveals clade-specific patterns of virulence, resistance, and secondary metabolism.
PMID:
43016185
Bibliographic data and abstract were imported from PubMed on 12 Nov 2026.
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