Tohoku University · Biochemistry, Genetics and Molecular Biology
Professor Shuhei Yabe's research lab specializes in the discovery and characterization of novel microbial taxa, particularly from extreme and understudied environments such as geothermal soils, compost, and polar ecosystems. The lab focuses on uncultured or poorly understood bacterial lineages—especially within the phylum *Chloroflexi* and the recently recognized *Ktedonobacteria*—to explore their ecological roles, physiological traits, and biotechnological potential, including the production of novel natural products and bioactive compounds. A key research direction involves developing molecular tools, such as 16S rRNA gene-targeted primers, to study microbial diversity and community structure in complex environments. The lab also emphasizes polyphasic taxonomy, combining genomics, physiology, and chemotaxonomy to describe new species with unique metabolic capabilities, such as thermophilic, spore-forming actinomycete-like bacteria and aerobic anoxygenic phototrophs.
Figures are computed from collected data and may differ slightly.
We isolated from compost an aerobic, thermophilic, Gram-stain-positive, spore-forming bacterium that formed branched vegetative and aerial mycelia. This strain, designated SK20-1T, grew at 31-58 degrees C, with optimum growth at 50 degrees C, while no growth was observed below 28 or above 60 degrees C. The pH range for growth was 5.4-8.7, with optimum growth at pH 7.0, while no growth was observed below pH 5.0 or above pH 9.1. Strain SK20-1T was able to hydrolyse polysaccharides such as cellulos
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. <i>Ktedonobacteria</i>, a class of deeply branched bacterial lineage in the ancient phylum <i>Chloroflexi</i>, are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate <i>Ktedonobacteria</i> as a potential act
Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplico
Two thermophilic, Gram-stain-positive, sporulating bacterial strains, which formed branched vegetative and aerial mycelia, were isolated from fallen leaves sampled from geothermal soils and designated ONI-1(T) and ONI-5(T). Strain ONI-1(T) grew at 50-74 °C, with optimum growth at 60-65 °C, and strain ONI-5(T) grew at 45-74 °C, with optimum growth at 60-65 °C. The pH range for growth of the strains was pH 4.6-8.0, with optimum growth at pH 7.0. The DNA G+C contents of strains ONI-1(T) and ONI-5(T
A mesophilic, Gram-stain-positive, spore-forming bacterium that formed branched mycelia was isolated from paddy soil in Gunung Salak (Mount Salak), West Java, Indonesia. This strain, designated S-27T, grew at temperatures between 20 and 37 °C; the optimum growth temperature was 25 to 30 °C, and no growth was observed at 15 or 45 °C. The pH range for growth was pH 3.5 to 8.6; the optimum pH was 6.0, and no growth was observed at pH 3.0 or 9.2. Strain S-27T was able to hydrolyse polysaccharides su
The previously uncultured phylum "Candidatus Eremiobacterota" is globally distributed and often abundant in oligotrophic environments. Although it includes lineages with the genetic potential for photosynthesis, one of the most important metabolic pathways on Earth, the absence of pure cultures has limited further insights into its ecological and physiological traits. We report the first successful isolation of a "Ca. Eremiobacterota" strain from a fumarolic ice cave on Mt. Erebus volcano (Antar
A thermophilic, Gram-stain-positive, spore-forming bacterium that formed branched vegetative and aerial mycelia was isolated from fallen leaves on geothermal soil. This strain, designated F4T, grew at temperatures between 30 and 60 °C; optimum growth temperature was 50 °C, whereas no growth was observed below 28 °C or above 65 °C. The pH range for growth was 4.9-9.5; the pH for optimum growth was 7.0, but no growth was observed at pH below 4.4 or above 10.0. Strain F4T was able to hydrolyse poly
A Gram-negative bacterium, designated CKTN2(T), was isolated from compost. Cells of strain CKTN2(T) were strictly aerobic rods. The isolate grew at 20-50 °C (optimum 40-45 °C), but not below 15 °C or above 52 °C, and at pH 5.9-8.8 (optimum pH 7.0), but not below pH 5.4 or above pH 9.3. The DNA G+C content was 40.3 mol%. The predominant menaquinone was MK-7. The major fatty acids were iso-C15 : 0 (45.2 %), iso-C17 : 0 3-OH (11.1 %) and C18 : 0 (14.5 %). Analysis of the 16S rRNA gene sequence of s
A novel extremely thermophilic bacterium (Ni80T) was isolated from food sludge compost in Japan. Cells were Gram-positive, spore-forming, strictly-aerobic and rod-shaped with peritrichous flagella. The novel isolate grew at pH 6.5-10.5 but not at pH 11.0 (optimum pH 8.0) and 52-79 degrees C but not 80 degrees C (optimum 70 degrees C). The strain could not grow in more than 1% NaCl. The G+C content of the genomic DNA is 72 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated tha
As far as known, sporulation modes in prokaryotes include formation of endospores exemplified by Firmicutes bacteria, myxospores by myxobacteria and arthrospores by actinomycetes. Here we describe Thermosporothrix hazakensis strain SK20-1(T) belonging to the phylum Chloroflexi with a life cycle including a novel prokaryotic sporulation mode. Microscopic observations showed that strain SK20-1(T) formed multiple exospores per mother cell by budding in branched aerial mycelia. Although branched aer
A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3(T), grew at temperatures between 35 and 62 °C, with optimum growth at 50-55 °C. No growth was observed below 29 °C or above 65 °C. The pH range for growth was 5.7-10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3(T) was 69.2 mol%. The major fatty acids found were C(15 : 0) iso (14.2
A Gram-stain-positive thermophilic bacterium, designated strain Nis3(T), was isolated from compost. The strain grew at 23-57 °C (optimum, 50 °C); no growth was observed below 15 or above 60 °C. The pH range for growth was 5.9-8.8 (optimum, 7.0); no growth was observed below pH 5.4 or above pH 9.3. The DNA G+C content of strain Nis3(T) was 63.4 mol%. The dominant quinone type was ubiquinone Q-10. The major fatty acids were C(18:1)ω7c, C(19:0)ω8c cyclo and C(18:0). The polar lipids comprised phosp
Currently, actinomycetes and myxobacteria are the only bacteria believed to form sporangia. Here, we describe a sporangium-forming process identified in Dictyobacter aurantiacus strain S27<sup>T</sup> belonging to the class Ktedonobacteria in the phylum Chloroflexi. Microscopic observations showed that strain S27<sup>T</sup> forms a substrate mycelium and subsequently produces globose or subglobose terminal sporangia arising from the vegetative mycelia through short stalk cells. This morphogenet
The aerobic, Gram-positive, mesophilic <i>Ktedonobacteria</i> strains, Uno17<sup>T</sup>, SOSP1-1<sup>T</sup>, 1-9<sup>T</sup>, 1-30<sup>T</sup> and 150040<sup>T</sup>, 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(H<sub>2</sub>
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