The prevalence of antibiotic resistance and the decrease in novel antibiotic discovery in recent years necessitates the identification of potentially novel microbial resources to produce natural products.
Ktedonobacteria
, a class of deeply branched bacterial lineage in the ancient phylum
Chloroflexi
, are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate
Ktedonobacteria
as a potential active producer of bioactive compounds. In this study, we observed the existence of a putative “megaplasmid,” multiple copies of ribosomal RNA operons, and high ratio of hypothetical proteins with unknown functions in the class
Ktedonobacteria
. Furthermore, a total of 104 antiSMASH-predicted putative biosynthetic gene clusters (BGCs) for secondary metabolites with high novelty and diversity were identified in nine
Ktedonobacteria
genomes. Our investigation of domain composition and organization of the non-ribosomal peptide synthetase and polyketide synthase BGCs further supports the concept that class
Ktedonobacteria
may produce compounds structurally different from known natural products. Furthermore, screening of bioactive compounds from representative
Ktedonobacteria
strains resulted in the identification of broad antimicrobial activities against both Gram-positive and Gram-negative tested bacterial strains. Based on these findings, we propose the ancient, ubiquitous, and spore-forming
Ktedonobacteria
as a versatile and promising microbial resource for natural product discovery.
An aerobic, Gram-stain-positive, mesophilic
Ktedonobacteria
strain, W12T, was isolated from soil of the Mt Zao volcano in Miyagi, Japan. Cells were filamentous, non-motile, and grew at 20–37 °C (optimally at 30 °C), at pH 5.0–7.0 (optimally at pH 6.0) and with <2 % (w/v) NaCl on 10-fold diluted Reasoner’s 2A (R2A) medium. Oval-shaped spores were formed on aerial mycelia. Strain W12T hydrolysed microcrystalline cellulose and xylan very weakly, and used d-glucose as its sole carbon source. The major menaquinone was MK-9, and the major cellular fatty acids were C16 : 1 2-OH, iso-C17 : 0, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and anteiso-C17 : 0. Cell-wall sugars were mannose and xylose, and cell-wall amino acids were d-glutamic acid, glycine, l-serine, d-alanine, l-alanine, β-alanine and l-ornithine. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain W12T has a genome of 7.42 Mb with 49.7 mol% G+C content. Nine copies of 16S rRNA genes with a maximum dissimilarity of 1.02 % and 13 biosynthetic gene clusters mainly coding for peptide products were predicted in the genome. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that strain W12T represents a novel species in the genus
Dictyobacter
. The most closely related
Dictyobacter
type strain was
Dictyobacter alpinus
Uno16T, with 16S rRNA gene sequence similarity and genomic average nucleotide identity of 98.37 % and 80.00 %, respectively. Herein, we propose the name Dictyobacter vulcani sp. nov. for the type strain W12T (=NBRC 113551T=BCRC 81169T) in the bacterial class
Ktedonobacteria
.
The aerobic, Gram-positive, mesophilic
Ktedonobacteria
strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus
Dictyobacter
, with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was
Ktedonobacter racemifer
SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinct clade within the order
Ktedonobacterales
, showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040T=CGMCC 1.17052T=BCRC 81202T) within the family Reticulibacteraceae fam. nov. in the order
Ktedonobacterales
; strain SOSP1-1T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1T=CGMCC 1.17205T=BCRC 81203T) and strain SOSP1-30T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30T=CGMCC 1.17733T=BCRC 81205T) within the family
Ktedonobacteraceae
; strain Uno17T as Dictyobacter arantiisoli sp. nov. (type strain Uno17T=NBRC 113155T=BCRC 81116T); and strain SOSP1-9T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9T=CGMCC 1.17206T=BCRC 81204T) within the family
Dictyobacteraceae
.
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