Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

A genome mining survey combined with metabolome analysis of publicly available strains identified Couchioplanes sp. RD010705, a strain belonging to an underexplored genus of rare actinomycetes, as a producer of new metabolites. HPLC-DAD-guided fractionation of its fermentation extracts resulted in the isolation of five new methyl-branched unsaturated fatty acids, (2E,4E)-2,4-dimethyl-2,4-octadienoic acid (1), (2E,4E)-2,4,7-trimethyl-2,4-octadienoic acid (2), (R)-(−)-phialomustin B (3), (2E,4E)-7-hydroxy-2,4-dimethyl-2,4-octadienoic acid (4), (2E,4E)-7-hydroxy-2,4,7-trimethyl-2,4-octadienoic acid (5), and one prenylated tryptophan derivative, 6-(3,3-dimethylallyl)-N-acetyl-ʟ-tryptophan (6). The enantiomer ratio of 4 was determined to be approximately S/R = 56:44 by a recursive application of Trost’s chiral anisotropy analysis and chiral HPLC analysis of its methyl ester. Compounds 1–5 were weakly inhibitory against Kocuria rhizophila at MIC 100 μg/mL and none were cytotoxic against P388 at the same concentration.

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

A genome mining survey combined with metabolome analysis of publicly available strains identified Couchioplanessp. RD010705, a strain belonging to an underexplored genus of rare actinomycetes, as a producer of new metabolites. HPLC-DAD-guided fractionation of its fermentation extracts resulted in the isolation of five new methyl-branched unsaturated fatty acids, (2E,4E)-2,4-dimethyl-2,4-octadienoic acid (1), (2E,4E)-2,4,7-trimethyl-2,4-octadienoic acid (2), (R)-(–)-phialomustin B (3), (2E,4E)-7-hydroxy-2,4-dimethyl-2,4-octadienoic acid (4), (2E,4E)-7-hydroxy-2,4,7-trimethyl-2,4-octadienoic acid (5), and one prenylated tryptophan derivative, 6-(3,3-dimethylallyl)-N-acetyl-L-tryptophan (6). The enantiomer ratio of 4 was determined to be approximately S/R = 56/44 by a recursive application of Trost’s chiral anisotropy analysis and chiral HPLC analysis of its methyl ester. Compounds 1–5 were weakly inhibitory against Kocuria rhizophila at MIC 100 mg/mL and none were cytotoxic against P388 at the same concentration.

Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental hole in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic decay through the pseudogenization of amino acids metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

Complete Genome Sequence Data of rare Actinomycetes Strain, Saccharothrix texasensis strain 6-C, a Biological Control Agent for Potato Late Blight

A rare actinomycetes strain of Saccharothrix texasensis strain 6-C, has been isolated from the potato rhizosphere and it was shown to act as a biological control agent to potato late blight. It is also the first report on Saccharothrix inhibiting P. infestans. Here, we present the complete genome data of S. texasensis strain 6-C, assembled by sequencing reads obtained by both PacBio and Illumina technologies with annotation. The final assembled genome length is 9,045,220 bp, with no gaps, no plasmid, and its GC content is 72.39%. Nine non-ribosomal peptide synthetase (NRPS), five type I polyketide synthase (T1PKS), four terpene and three lanthipeptide gene clusters were identified in the genome, which would be likely to encode lots of antimicrobial active substances to help host plants against disease. This genome sequence could contribute to investigations of the molecular basis underlying the biocontrol activity of this Saccharothrix strain.

Enhanced polyhydroxybutyrate (PHB) production by newly isolated rare actinomycetes Rhodococcus sp. strain BSRT1-1 using response surface methodology

Poly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and 1H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.

SELECTIVE ISOLATION OF Dactylosporangium AND Micromonospora FROM THE SOIL OF KARST CAVE OF SIMEULUE ISLAND AND THEIR ANTIBACTERIAL POTENCY

Karst is a unique ecosystem that consists of a thin soil layer on the carbonate rocks. It has a diverse microorganism, especially actinomycetes group, which might potentially produce beneficial secondary metabolites that remain unknown. In this study, we were interested in isolating Dactylosporangium and Micromonospora that have been potentially reported as antibiotic sources. We used two methods using the chemical germicide (pretreatment 1.5% phenol) compared with the SDS-YE (0.05% SDS pretreatment). Thirty-nine isolates actinomycetes were successfully isolated from two samples of the karst cave soils. Thirteen isolates were obtained by using the germicide chemical method and closely related to the genera of Dactylosporangium and Micromonospora. On the other hand, the SDS-YE grew twenty-six isolates which closely related to 11 genera of actinomycetes (Catenulispora, Nocardia, Rhodococcus, Ornithinimicrobium, Catellatospora, Dactylosporangium, Micromonospora, Streptacidiphilus, Streptomyces, Nonomuraea, and Streptosporangium). These results suggest that 1.5% of phenol pretreatment could preserve the genera of Dactylosporangium and Micromonospora, while the Streptomyces and other rare actinomycetes were killed. Among all isolates, only 7 showed the antibacterial activity on tested bacteria. Even though the antibacterial activity of those isolates was not high, the isolation of actinomycetes from a specific substrate is necessary to be conducted on exploring the richness of our natural resources.

Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans

(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.