Frontier for Search for New Secondary Metabolites

May 29, 2026

Biosynthetic gene clusters accumulate on large extrachromosomal DNAs in mycelium-forming bacteria

An international collaborative research group led by RIKEN CSRS demonstrated that Ktedonobacteria in mycelium-forming bacteria, which are widely distributed in terrestrial soils, harbor various biosynthetic gene clusters (BGCs) that can produce candidate substances for medical and agricultural use, which are accumulated on large extrachromosomal (chromid-like) DNAs.

The research group focused on volcanic regions, one of the main habitats of Ktedonobacteria, where unexplored soil bacteria might live. The group analyzed the genomes of bacterial strains newly isolated from soil samples collected from the volcanic Mount Zao (Japan), which has extensive volcanic barren soil. The obtained data were integrated with metagenomic information from the same soils and with genomic information from the public database to perform comparative analyses of 183 Ktedonobacterial genomes. The researchers discovered that about a quarter of the genomes harbor diverse BGCs, and many of the detected BGCs show significant phylogenetic differences from those registered in the existing database. They also found that these BGCs exist concentratively on chromid-like DNAs. These results suggest that current metagenomic analyses might have overlooked or failed to properly retrieve such large extrachromosomal DNAs, highlighting the importance of genomic analyses based on cultivated strains.

The findings of this study show that Ktedonobacteria can be a frontier for the search for new secondary metabolites that may compliment the currently mainstream actinomycetes. It is expected that the elucidation of the functions of BGCs accumulated on chromid-like DNAs will advance the exploration for unknown beneficial compounds and candidate substances for medical and agricultural use.

Original article: mSystems　doi: 10.1128/msystems.00197-26; S. Yabe, Y. Zheng, S. Takahashi, C. Yang, Y. Nose, S. Yamazaki, N. Okuma, M. K. Rachmania, F. Ningsih, W. Sjamsuridzal, M. Sato, K. Toyooka, Y. Ichihashi,; "Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria".
Contact: Shuhei Yabe; Research Scientist
Yasunori Ichihashi; Team Director
Holobiont and Resilience Research Team