Duangupama, Thitikorn

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Duangupama, Thitikorn
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thitikorn.du@kmitl.ac.th

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    Micromonospora solifontis sp. nov., an actinobacterium isolated from hot spring soil
    (2023-05-01)
    Duangupama, Thitikorn
    ;
    Pansomsuay, Rawirat
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    An actinobacterium strain, PPF5-17<sup>T</sup>, 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 PPF5-17<sup>T</sup> 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). PPF5-17<sup>T</sup> 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> . PPF5-17<sup>T</sup> shared the highest 16S rRNA gene sequence similarity with Micromonospora fluminis LMG 30467<sup>T</sup> (99.3%). A genome-based taxonomic study revealed that PPF5-17<sup>T</sup> was closely related to Micromonospora aurantinigra DSM 44815<sup>T</sup> 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, PPF5-17<sup>T</sup> could be distinguished from its closest neighbours, M. fluminis LMG 30467<sup>T</sup> and M. aurantinigra DSM 44815<sup>T</sup>, with respect to a broad range of phenotypic properties. Thus, PPF5-17<sup>T</sup> represents a novel species, for which the name Micromonospora solifontis sp. nov. is proposed. The type strain is PPF5-17<sup>T</sup> (= TBRC 8478<sup>T</sup> = NBRC 113441<sup>T</sup>).
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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
    ;
    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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    Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum
    (2023-06-01)
    Pansomsuay, Rawirat
    ;
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    An endophytic actinobacterium, designated strain PLAI 1-29<sup>T</sup>, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29<sup>T</sup> was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus Streptomyces. Strain PLAI 1-29<sup>T</sup> 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 1-29<sup>T</sup> 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 1-29<sup>T</sup> 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 S187<sup>T</sup>. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29<sup>T</sup> and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29<sup>T</sup> (=TBRC 7645<sup>T</sup>=NBRC 113170<sup>T</sup>) is considered to represent a new Streptomyces species, for which we propose the name Streptomyces zingiberis sp. nov.
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    Micromonospora thermarum sp. nov., an actinobacterium isolated from hot spring soil
    (2023-04-01)
    Pansomsuay, Rawirat
    ;
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    An actinomycete, designated strain HSS6-12<sup>T</sup>, 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. HSS6-12<sup>T</sup> 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 HSS6-12<sup>T</sup> shared the highest 16S rRNA gene sequence similarity with Micromonospora inositola DSM 43819<sup>T</sup> (99.3%). In contrast, the genome analysis showed that HSS6-12<sup>T</sup> formed a tight taxonomic position in a phylogenomic tree with Micromonospora endolithica DSM 44398<sup>T</sup>. Moreover, the average nucleotide identity-blast, the digital DNA-DNA hybridization, and the average amino acid identity values between HSS6-12<sup>T</sup> and M. inositola DSM 43819<sup>T</sup> and M. endolithica DSM 44398<sup>T</sup> were 83.1–84.0%, 27.5–28.7%, and 80.4–82.2%, respectively, indicating that HSS6-12<sup>T</sup> was different species with both closely related Micromonospora-type strains. In addition, HSS6-12<sup>T</sup> could be discriminated from its closely related type strains by many physiological and biochemical characteristics. Thus, HSS6-12<sup>T</sup> could be considered a novel species of the genus Micromonospora, and the name Micromonospora thermarum is proposed for the strain. The type strain is HSS6-12<sup>T</sup> (= BCC 41915<sup>T</sup> = JCM 17127<sup>T</sup>).
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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
    ;
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    An actinobacterium strain, SW21<sup>T</sup>, 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 SW21<sup>T</sup> to the genus Gordonia and showed that Gordonia mangrovi KCTC 49383<sup>T</sup> (98.7%) was the closest relative. Moreover, the average nucleotide identity-blast (85.5%) and digital DNA–DNA hybridization (30.7%) values between strain SW21<sup>T</sup> 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 SW21<sup>T</sup> is representative of novel species of the genus Gordonia. The name Gordonia aquimaris sp. nov. is proposed for strain SW21<sup>T</sup>. The type strain is SW21<sup>T</sup> (=TBRC 15691<sup>T</sup>=NBRC 115558<sup>T</sup>).