2026-05-29 理化学研究所
研究概要
＜関連情報＞
- https://www.riken.jp/press/2026/20260529_2/index.html
- https://journals.asm.org/doi/10.1128/msystems.00197-26
クテドノバクテリアにおける生合成遺伝子クラスターの予測される重要な部位としてのクロミド様二次レプリコン Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria
Shuhei Yabe, Yu Zheng, Shunji Takahashi, Chongyang Yang, Yui Nose, Shinichi Yamazaki, Nao Okuma, +13 , Yasunori Ichihashi
mSystems Published:29 May 2026
DOI:https://doi.org/10.1128/msystems.00197-26
ABSTRACT
Soils harbor immense biosynthetic gene cluster (BGC) diversity that mediates microbial interactions, yet this potential remains unevenly mapped and poorly characterized across diverse bacterial lineages. Ktedonobacteria (phylum Chloroflexota) are an actinomycete-like lineage widely distributed in terrestrial soils, including oligotrophic volcanic deposits; however, their secondary metabolism and genome architecture remain poorly characterized. Here, we integrate targeted cultivation from volcanic soils at Mount Zao (Japan) with genome-resolved metagenomics and comparative analysis of public genomes to examine biosynthetic potential across 183 ktedonobacterial genomes. We identified 1,546 BGCs and grouped them into 1,162 non-redundant gene-cluster families (GCFs) using antiSMASH and BiG-SLiCE. Nearly one quarter of genomes encoded ≥10 distinct GCFs, and several family-level clades exhibited high GCF richness that approached that of Streptomyces within our data set, highlighting a putatively biosynthetically rich yet underexplored soil bacterial lineage. Most ktedonobacterial BGCs were highly divergent from current reference collections and exhibited unusually low intra-genomic redundancy, suggesting broad putative chemical diversity. Long-read assemblies from 10 cultured strains revealed recurrent 1.6–3.5 Mb ECE-like contigs with chromid-like features, but distinct maintenance features. These replicons were consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the phylogenetic landscape of soil biosynthetic diversity and highlight ECE-like contigs as major genomic reservoirs for secondary metabolism in Ktedonobacteria.
