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Genome Characterization for the Antimicrobial Potential of Streptomyces samsunensis SA31, a Rhizospheric Actinomycete of Cymbopogon citratus (DC) Stapf.
(2025-01-01)
Wongsariya, Karn
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Duangupama, Thitikorn
;
Pansomsuay, Rawirat
;
Thanaboripat, Dusanee
;
Thawai, Chitti
Streptomyces species are promising resources of bioactive compounds that play a vital role in medicinal biotechnology. Streptomyces sp. SA31 was isolated from the rhizospheric soil of Cymbopogon citratus (DC) Stapf. The strain was identified as Streptomyces samsunensis based on genome-based taxonomic analysis. The draft genome of strain SA31 contained 11,850,342 bp with a high percentage of G+C at 71.0% and carried 9,350 predicted protein-encoding sequences (CDSs). Furthermore, the secondary metabolite biosynthesis gene clusters in the genome of strain SA31 were predicted by antiSMASH. In silico analysis showed 71 predicted biosynthetic gene clusters (BGCs) responsible for antimicrobial secondary metabolite synthesis. Most gene clusters were involved in the biosynthesis of polyketide synthase. The genome of strain SA31 harbored seven types of polyketide biosynthesis gene clusters that might be associated with antimicrobial activity. Additionally, the genome of strain SA31 contained unexplored secondary metabolite biosynthesis gene clusters. In vitro antimicrobial assay showed that an ethyl acetate extract from the culture broth of strain SA31 could inhibit the growth of Staphylococcus aureus ATCC 25923, Kocuria rhizophila ATCC 9341, Bacillus subtilis ATCC 6633, Candida albicans ATCC 10231, and Aspergillus flavus IMI 242684, implying that the genome of strain SA31 contained potential BGCs for the production of antimicrobial secondary metabolites and led to the isolation of geldanamycin and 17-O-demethylgeldanamycin. Therefore, it can be proved that the rhizosphere-associated soil of C. citratus (DC) Stapf. is a rich habitat for actinomycetes that are capable of producing promising biologically active compounds.
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Pradimicin U, a promising antimicrobial agent isolated from a newly found Nonomuraea composti sp. nov
(2024-12-01)
Duangupama, Thitikorn
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
;
Tadtong, Sarin
Pradimicin U is a new dihydrobenzo[a]naphthacenequinone compound found to be active on a screen designed to investigate compounds with antimicrobial activity, produced by the actinomycete designated strain FMUSA5-5T. The strain was isolated from a bio-fertilizer of Musa spp. collected from Suphanburi province, Thailand. The chemotaxonomic characteristics and 16S rRNA gene analysis revealed that strain FMUSA5-5T is a member of the genus Nonomuraea. Low genome-based taxonomic criteria, average nucleotide identity (ANI) (82.8–88.3%), average amino-acid identity (AAI) (79.4–87.3%), and digital DNA–DNA hybridization (dDDH) (29.5–38.5%) values and several phenotypic differences between strain FMUSA5-5T and its closest type strains of the genus Nonomuraea indicated that strain FMUSA5-5T represents a novel species of the genus Nonomuraea and the name Nonomuraea composti sp. nov. is proposed for the strain. The crude extract from the culture broth of strain FMUSA5-5T displayed promising antimicrobial activity against several pathogens and led to the isolation of a novel secondary metabolite, pradimicin U. Interestingly, this compound displayed a broad spectrum of biological activities such as antimalarial activity against Plasmodium falciparum K1 (IC<inf>50</inf> value = 3.65 µg/mL), anti-Mycobacterium tuberculosis H37Ra (MIC value = 25.0 µg/mL), anti-Alternaria brassicicola BCC 42724 (MIC value = 25.0 µg/mL), anti-Bacillus cereus ATCC 11778 and anti-Staphylococcus aureus ATCC 29213 (MIC values = 6.25 and 1.56 µg/mL, respectively). Moreover, the compound possessed strong anti-human small cell lung cancer (NCI-H187) activity with IC<inf>50</inf> value of 5.69 µg/mL, while cytotoxicity against human breast cancer (MCF-7) and Vero cells was very weak (IC<inf>50</inf> values of 52.49 and 21.84 µg/mL, respectively).
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Description of Streptomyces siderophoricus sp. nov., a promising nocardamine-producing species isolated from the rhizosphere soil of Mangifera indica
(2024-11-01)
Duangupama, Thitikorn
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
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Tadtong, Sarin
An actinomycete, designated strain CH9-7T, was isolated from the rhizosphere soil of Mangifera indica. The morphological and chemotaxonomic properties, such as the production of spiral spore chains and the presence of LL-diaminopimelic acid in the peptidoglycan, showed that it belongs to the genus Streptomyces. Based on the 16S rRNA gene analysis, it was confirmed that strain CH9-7T was a member of the genus Streptomyces and revealed 99.9% 16S rRNA gene sequence similarity to its closest relative strains, Streptomyces lydicus NBRC 13058 T and Streptomyces chattanoogensis NBRC 12754 T. Although the strain showed high 16S rRNA gene sequence similarity values, however, genome relatedness indexes exhibited that the average nucleotide identity based on the MUMmer (ANIm) algorithm, the average amino acid identity (AAI), and the digital DNA–DNA hybridization values between strain CH9-7T and its closest phylogenomic relatives were below the threshold values for delineation of a novel species, (ANIm ranging from 87.5 to 88.6, AAI ranging from 80.6 to 84.6, and dDDH ranging from 28.4 to 31.7), respectively. A taxonomic position of strain CH9-7T in the phylogenomic tree showed that the closest relative strain was S. lydicus NBRC 13058 T. The comparative phenotypic studies between strain CH9-7T and its closest relatives revealed that strain CH9-7T could be classified as a novel species of the genus Streptomyces. Thus, the name Streptomyces siderophoricus sp. nov. is proposed for the strain. The type strain is CH9-7T (= TBRC 17833 T = NBRC 116426 T). The chemical investigation led to the isolation of four known compounds (compounds 1-4). Among these compounds, compound 1 was identified to be nocardamine, a promising bioactive substance.
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Genome Insights into the Plant Growth Promoting Features of a Newly Found Microbispora sp. SCL1-1
(2024-10-02)
Dejtisakdi, Wipawee
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Duangupama, Thitikorn
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Thawai, Chitti
Plant growth-promoting (PGP) actinobacteria can be used to promote plant growth. Their use is a promising strategy that can be employed instead of agricultural chemical fertilizers. An actinobacterium strain, designated SCL1-1, was collected and isolated from a soil sample in a herbal garden at Pathum Thani province, Thailand. Analysis revealed that the SCL1-1 strain was a Gram-positive bacterium that formed longitudinal paired spores that were borne directly on aerial mycelia. It contained meso-diaminopimelic acid in its cell wall peptidoglycan. Moreover, madurose, which is a diagnostic sugar, was present in its whole-cell hydrolysates. 16S rRNA gene analysis revealed that the SCL1-1 strain was a member of the Microbispora and showed a close relationship to Microbispora rosea ATCC 12950T (99.6%), followed by Microbispora hainanensis DSM 45428T (99.2%). However, a genome-based polyphasic study revealed that strain SCL1-1 had a low average nucleotide identity (ANI) (<95%), and digital DNA–DNA hybridization (dDDH) value (<70%) with M. rosea ATCC 12950T and M. hainanensis DSM 45428T, indicating that strain SCL1-1 was a different species to its close relatives. Genome mining of strain SCL1-1 showed the presence of genes related to the production of indole-3-acetic acid (IAA), and siderophore, which are agents that promote plant growth. In addition, the genome of strain SCL1-1 was found in several secondary metabolite biosynthetic gene clusters, which were possibly encoded for a broad range of remarkable natural products and antibiotics.
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New insights into the neuroprotective and beta-secretase1 inhibitor profiles of tirandamycin B isolated from a newly found Streptomyces composti sp. nov.
(2023-12-01)
Duangupama, Thitikorn
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Pratuangdejkul, Jaturong
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Chongruchiroj, Sumet
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
Tirandamycin (TAM B) is a tetramic acid antibiotic discovered to be active on a screen designed to find compounds with neuroprotective activity. The producing strain, SBST2-5T, is an actinobacterium that was isolated from wastewater treatment bio–sludge compost collected from Suphanburi province, Thailand. Taxonomic characterization based on a polyphasic approach indicates that strain SBST2-5T is a member of the genus Streptomyces and shows low average nucleotide identity (ANI) (81.7%), average amino-acid identity (AAI) (78.5%), and digital DNA-DNA hybridization (dDDH) (25.9%) values to its closest relative, Streptomyces thermoviolaceus NBRC 13905T, values that are significantly below the suggested cut-off values for the species delineation, indicating that strain SBST2-5T could be considered to represent a novel species of the genus Streptomyces. The analysis of secondary metabolites biosynthetic gene clusters (smBGCs) in its genome and chemical investigation led to the isolation of TAM B. Interestingly, TAM B at 20 µg/mL displayed a suppressive effect on beta-secretase 1 (BACE1) with 68.69 ± 8.84% inhibition. Molecular docking simulation reveals the interaction mechanism between TAM B and BACE1 that TAM B was buried in the pocket of BACE-1 by interacting with amino acids Thr231, Asp 228, Gln73, Lys 107 via hydrogen bond and Leu30, Tyr71, Phe108, Ile118 via hydrophobic interaction, indicating that TAM B represents a potential active BACE1 inhibitor. Moreover, TAM B can protect the neuron cells significantly (% neuron viability = 83.10 ± 9.83% and 112.72 ± 6.83%) from oxidative stress induced by serum deprivation and Aβ<inf>1–42</inf> administration models at 1 ng/mL, respectively, without neurotoxicity on murine P19-derived neuron cells nor cytotoxicity against Vero cells. This study was reportedly the first study to show the neuroprotective and BACE1 inhibitory activities of TAM B.
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Streptomyces telluris sp. nov., a promising terrestrial actinobacterium with antioxidative potentials
(2023-06-01)
Thayanuwadtanawong, Onnicha
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Duangupama, Thitikorn
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Bunbamrung, Nantiya
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
An actinomycete strain, AA8T, which produced a long straight chain of spores (verticillati type), was isolated from the rhizosphere soil of Mangifera indica in Bangkok, Thailand. A polyphasic taxonomic study was carried out to establish the taxonomic position of the strain. Strain AA8T formed a tight taxonomic position in the 16S rRNA gene tree with Streptomyces roseifaciens MBT76T. In contrast, the genome-based taxonomic analysis showed that strain AA8T shared low average nucleotide identity-BLAST (94.1%), the digital DNA–DNA hybridization (58.2%), and the average amino acid identity (93.6%) values with S. roseifaciens MBT76T. Moreover, a combination of physiological and biochemical properties indicated that strain AA8T was distinguished from all Streptomyces species with effectively published names. Strain AA8T, therefore, represents a novel species of Streptomyces, and the name Streptomyces telluris is proposed for the strain. The type strain is AA8T (= TBRC 8483T = NBRC 113461T). The chemical investigation led to the isolation of nine known compounds (compounds 1–9). Among these compounds, compound 7 (3,4-dihydroxybenzaldehyde) possesses strong antioxidant activity equal to ascorbic acid, a powerful antioxidative agent.
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Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum
(2023-06-01)
Pansomsuay, Rawirat
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Duangupama, Thitikorn
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
An endophytic actinobacterium, designated strain PLAI 1-29T, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29T was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus Streptomyces. Strain PLAI 1-29T produced a spiral spore chain on aerial mycelium and grew at 15–40 °C, pH 6–10 on International Streptomyces Project 2 agar. The maximum NaCl concentration for growth was 9% (w/v). Cells of strain PLAI 1-29T presented ll-diaminopimelic acid, arabinose, galactose and ribose. The detected phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphati-dylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H<inf>6</inf>) and MK-9(H<inf>8</inf>). The major cellular fatty acids were iso-C<inf>16:0</inf>, anteiso-C<inf>15:0</inf> and anteiso-C<inf>17:0</inf> . The genome-based taxonomic details revealed the assignment of strain PLAI 1-29T to the genus Streptomyces and exhibited low threshold values for the delineation of a novel species by average nucleotide identity–blast (84.0%), average amino acid identity (80.0%) and digital DNA–DNA hybridization (27.6%) with its closest type strain, Streptomyces xinghaiensis S187T. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29T and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29T (=TBRC 7645T=NBRC 113170T) is considered to represent a new Streptomyces species, for which we propose the name Streptomyces zingiberis sp. nov.
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Micromonospora solifontis sp. nov., an actinobacterium isolated from hot spring soil
(2023-05-01)
Duangupama, Thitikorn
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Pansomsuay, Rawirat
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
An actinobacterium strain, PPF5-17T, was isolated from hot spring soil collected from Chiang Rai province, Thailand. The strain exhibited morphological and chemotaxonomic properties similar to those of members of the genus Micromonospora. Colonies of PPF5-17T were strong pinkish red and turned black after sporulation in ISP 2 agar medium. Cells formed single spores directly on the substrate mycelium. Growth was observed from 15 to 45 °C and at pH 5–8. Maximum NaCl concentration for growth was 3% (w/v). PPF5-17T was found to have meso-diaminopimelic acid, xylose, mannose and glucose in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides were observed as the membrane phospholipids. MK-10(H<inf>6</inf> ), MK-9(H<inf>6</inf> ), MK-10(H<inf>4</inf> ) and MK-9(H<inf>4</inf> ) were the major menaquinones. The predominant cellular fatty acids were iso-C<inf>15:0</inf>, iso-C<inf>17:0</inf>, anteiso-C<inf>17:0</inf> and iso-C<inf>16:0</inf> . PPF5-17T shared the highest 16S rRNA gene sequence similarity with Micromonospora fluminis LMG 30467T (99.3%). A genome-based taxonomic study revealed that PPF5-17T was closely related to Micromonospora aurantinigra DSM 44815T in the phylogenomic tree with an average nucleotide identity by blast (ANIb) of 87.7% and a digital DNA–DNA hybridization (dDDH) value of, 36.1% which were below the threshold values for delineation of a novel species. Moreover, PPF5-17T could be distinguished from its closest neighbours, M. fluminis LMG 30467T and M. aurantinigra DSM 44815T, with respect to a broad range of phenotypic properties. Thus, PPF5-17T represents a novel species, for which the name Micromonospora solifontis sp. nov. is proposed. The type strain is PPF5-17T (= TBRC 8478T = NBRC 113441T).
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Micromonospora thermarum sp. nov., an actinobacterium isolated from hot spring soil
(2023-04-01)
Pansomsuay, Rawirat
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Duangupama, Thitikorn
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
An actinomycete, designated strain HSS6-12T, was isolated from hot spring sediment collected from Ranong province, Thailand. The strain showed taxonomic characteristics consistent with those of members of the genus Micromonospora. HSS6-12T produced a single spore directly on the substrate mycelium, and no aerial mycelium was detected. The isomer of diamino acid presented in cell wall peptidoglycan was meso-diaminopimelic acid. Arabinose, xylose, glucose, and ribose were detected in whole-cell hydrolysates. MK-10(H<inf>4</inf>), MK-9(H<inf>4</inf>), and MK-10(H<inf>6</inf>) were major menaquinones. Major cellular fatty acids were iso-C<inf>16:0</inf>, iso-C<inf>15:0</inf>, and iso-C<inf>17:0</inf>. Phospholipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositolmannosides. 16S rRNA gene analysis revealed that HSS6-12T shared the highest 16S rRNA gene sequence similarity with Micromonospora inositola DSM 43819T (99.3%). In contrast, the genome analysis showed that HSS6-12T formed a tight taxonomic position in a phylogenomic tree with Micromonospora endolithica DSM 44398T. Moreover, the average nucleotide identity-blast, the digital DNA-DNA hybridization, and the average amino acid identity values between HSS6-12T and M. inositola DSM 43819T and M. endolithica DSM 44398T were 83.1–84.0%, 27.5–28.7%, and 80.4–82.2%, respectively, indicating that HSS6-12T was different species with both closely related Micromonospora-type strains. In addition, HSS6-12T could be discriminated from its closely related type strains by many physiological and biochemical characteristics. Thus, HSS6-12T could be considered a novel species of the genus Micromonospora, and the name Micromonospora thermarum is proposed for the strain. The type strain is HSS6-12T (= BCC 41915T = JCM 17127T).
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Gordonia aquimaris sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand
(2023-03-01)
Pansomsuay, Rawirat
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Duangupama, Thitikorn
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Pittayakhajonwut, Pattama
;
Intaraudom, Chakapong
;
Suriyachadkun, Chanwit
An actinobacterium strain, SW21T, was isolated from seawater collected in the upper Gulf of Thailand. Cells were Gram-stain-positive, aerobic and rod-shaped. Growth was observed from 15 to 37 °C and at pH 6–8. Maximum NaCl for growth was 14% (w/v). meso-Diaminopimelic acid, arabinose, galactose, glucose, rhamnose and ribose were detected in the whole-cell hydro-lysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside were detected as the phospholipids in the cells. The major menaquinones were MK-9(H<inf>2</inf> ) and MK-7(H<inf>2</inf> ). The major cellular fatty acids were C<inf>16:0</inf>, C<inf>18:1</inf> ω9c, C<inf>18:0</inf> and C<inf>18:0</inf> 10-methyl (TBSA). The 16S rRNA gene sequence data supported the assignment of strain SW21T to the genus Gordonia and showed that Gordonia mangrovi KCTC 49383T (98.7%) was the closest relative. Moreover, the average nucleotide identity-blast (85.5%) and digital DNA–DNA hybridization (30.7%) values between strain SW21T and its closest neighbour were below the threshold values for delineation of a novel species. The combination of genotypic and phenotypic data indicated that strain SW21T is representative of novel species of the genus Gordonia. The name Gordonia aquimaris sp. nov. is proposed for strain SW21T. The type strain is SW21T (=TBRC 15691T=NBRC 115558T).

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