Diversity analysis of actinomycetes from the gut of Pheretima aspergillum and bioactive secondary metabolites from an anti-Enterococcus faecalis strain

Background Antimicrobial resistance is one of the most pressing global public health challenges, with vancomycin-resistant Enterococcus (VRE) listed as a high-priority pathogen by the World Health Organization. Animal gut environments harbor actinomycetes with unique biosynthetic potential due to long-term coevolution with hosts. Pheretima aspergillum , a medicinal earthworm used in traditional Chinese medicine, continuously ingests complex organic substrates, creating selective pressures that may drive the evolution of novel secondary metabolic pathways in its gut symbionts. However, the diversity, culturable resources, and anti-VRE potential of gut actinomycetes from P. aspergillum remain largely unexplored. Results This study presents the first systematic characterization of the gut actinomycete diversity of P. aspergillum . High-throughput 16 S ribosomal RNA (16 S rRNA) amplicon sequencing revealed that the gut bacterial community of P. aspergillum is highly diverse, comprising 21 phyla, 75 classes, 141 orders, 263 families, 501 genera, and 608 putative species. Actinomycetota ranked as the third most dominant phylum (10.2% relative abundance). A total of 414 culturable gut-associated bacterial isolates were recovered using eight culture media, of which 332 (80.2%) were actinomycetes; 26 of the 414 isolates (6.3%) were identified as putative novel species. Strain CB1-10-1, identified as Streptomyces chartreusis , exhibited broad-spectrum antimicrobial activity against vancomycin-resistant Enterococcus faecalis (VREfa) and other pathogens. Whole-genome sequencing and genome mining identified 38 biosynthetic gene clusters (BGC). One type II polyketide synthase cluster showed a high-confidence match to the characterized benastatin BGC (BGC0000204.5). Integrated metabolomic analysis further confirmed the production of benastatin analogues. Guided by this multi-omics strategy, benastatin B and benastatin C were isolated and structurally identified, representing the first report of benastatin production by S. chartreusis . Moreover, this study is the first to demonstrate that benastatin B exhibits potent anti-VREfa activity, with a minimum inhibitory concentration of 2 µg/mL and a minimum bactericidal concentration of 4 µg/mL – both superior to vancomycin – and it shows bactericidal properties. Conclusions This study establishes P. aspergillum as a productive source of actinomycete diversity harboring potential novel species. The multi-omics-guided discovery approach led to the identification of benastatin B as a promising bactericidal lead compound against VREfa infections, providing proof-of-concept for the value of animal symbiotic actinomycetes in antimicrobial drug discovery and a foundation for future mechanistic and preclinical studies.