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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    Description of Streptomyces siderophoricus sp. nov., a promising nocardamine-producing species isolated from the rhizosphere soil of Mangifera indica
    (2024-11-01)
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    ;
    Tadtong, Sarin
    An actinomycete, designated strain CH9-7<sup>T</sup>, 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 CH9-7<sup>T</sup> 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 <sup>T</sup> and Streptomyces chattanoogensis NBRC 12754 <sup>T</sup>. 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 CH9-7<sup>T</sup> 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 CH9-7<sup>T</sup> in the phylogenomic tree showed that the closest relative strain was S. lydicus NBRC 13058 <sup>T</sup>. The comparative phenotypic studies between strain CH9-7<sup>T</sup> and its closest relatives revealed that strain CH9-7<sup>T</sup> 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 CH9-7<sup>T</sup> (= TBRC 17833 <sup>T</sup> = NBRC 116426 <sup>T</sup>). 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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    Streptomyces sennicomposti sp. nov., an actinomycete isolated from compost of Senna siamea (Lam.)
    (2022-01-01)
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    ;
    Sirirote, Pramote
    A member of the genus Streptomyces, designated RCPT1-4<sup>T</sup>, was isolated from compost of Senna siamea (Lam.), collected from an agricultural area in Rayong province, Thailand. The spore morphology and the presence of ll-diaminopimelic acid in the peptidoglycan indicate that RCPT1-4<sup>T</sup> shows the typical properties of members of the genus Streptomyces. On the basis of the results of 16S rRNA gene sequence analysis, the strain should be classified as representing a member of the genus Streptomy-ces and was most closely related to Streptomyces fumigatiscleroticus NBRC 12999<sup>T</sup> with the highest 16S rRNA gene sequence similarity of 99.2%, followed by Streptomyces spiralis NBRC 14215<sup>T</sup> (99.0%). In addition, RCPT1-4<sup>T</sup> shared the highest average nucleotide identity by blast (ANIb) (86.0%), and digital DNA–DNA hybridization (dDDH) (32.1%) values with S. spiralis NBRC 14215<sup>T</sup>. Furthermore, several physiological and biochemical differences were observed between RCPT1-4<sup>T</sup> and the closely related type strains of species with validly published names. These taxonomic data indicated that RCPT1-4<sup>T</sup> could be considered to represent a novel species of the genus Streptomyces and the name Streptomyces sennicomposti sp. nov. is proposed for this strain. The type strain is RCPT1-4<sup>T</sup> (=TBRC 11260<sup>T</sup>=NBRC 114303<sup>T</sup>).
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    Nocardia coffeae sp. nov., an endophytic actinobacterium isolatefrom the root of Coffea arabica (L.)
    (2022-01-01)
    Nammali, Achararak
    ;
    Duangupama, Thitikorn
    ;
    Suriyachadkun, Chanwit
    ;
    Tanasupawat, Somboon
    ;
    Thawai, Chitti
    The polyphasic taxonomic study of a novel endophytic actinobacterium strain (CA2R105<sup>T</sup>) was carried out. The strain formed fragmented substrate mycelium and showed chemotaxonomic properties typical of members of the genus Nocardia, i.e. the presence of mycolic acid and MK-8 (H<inf>4ω-cycl</inf> ) in its cells. Strain CA2R105<sup>T</sup> exhibited the highest 16S rRNA gene sequence similarity to Nocardia jiangxiensis NBRC 101359<sup>T</sup> (99.2%). The genome-based taxonomic analysis revealed low average nucleotide identity-blast and digital DNA–DNA hybridization values (<93.7, and <65.2%, respectively) to its closest relative. Moreover, many different phenotypic characteristics were observed between strain CA2R105<sup>T</sup> and all related Nocardia-type strains. This taxonomic evidence suggested that strain CA2R105<sup>T</sup> should be judged as representing a novel species of the genus Nocardia and the name, Nocardia coffeae sp. nov. is proposed. The type strain is CA2R105<sup>T</sup> (=TBRC 11247<sup>T</sup>=NBRC 114292<sup>T</sup>).
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    Streptomyces musisoli sp. nov., an actinomycete isolated from soil
    (2021-01-01)
    Duangupama, Thitikorn
    ;
    Intaraudom, Chakapong
    ;
    Pittayakhajonwut, Pattama
    ;
    Suriyachadkun, Chanwit
    ;
    Tadtong, Sarin
    An actinobacterium, strain CH5-8<sup>T</sup>, which formed spiral chains of spore arising from the aerial mycelium, was isolated from rhizosphere soil of Musa spp. The organism exhibited vivid greenish yellow substrate mycelium and easily produced the medium grey aerial spore mass on ISP2 medium. The typical chemotaxonomic properties of members of the genus Streptomyces were observed for strain CH5-8<sup>T</sup>, e.g. ll-diaminopimelic acid in cell peptidoglycan, MK-9(H<inf>8</inf>), MK-9(H<inf>6</inf>), and MK-9(H<inf>4</inf>) as major menaquinones and anteiso-C<inf>15:0</inf>, iso-C<inf>16:0</inf>, and anteiso-C<inf>17:0</inf> as major fatty acids. Diphosphatidylglycerol, phosphatidylethanola-mine, hydroxyphosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside were detected in the cells. A combination of morphological and chemotaxonomic data supported the assignment to the genus Strep-tomyces. The analysis result obtained for the 16S rRNA gene sequence confirmed the taxonomic affiliation at the genus level of this strain. The novel strain CH5-8<sup>T</sup> showed the highest 16S rRNA gene sequence values to Streptomyces echinatus NBRC 12763<sup>T</sup> (98.9%), followed by Streptomyces actinomycinicus RCU-197<sup>T</sup> (98.9%). The average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization values between CH5-8<sup>T</sup> and its closest relatives, S. echinatus CECT 3313<sup>T</sup> and S. actinomycinicus RCU-197<sup>T</sup>, were ≤91.6% and ≤47.4%, respectively. The digital DNA G+C content of genomic DNA was 72.1 mol%. On the basis of these phenotypic and genotypic data, strain CH5-8<sup>T</sup> represents a novel species, for which the name Streptomyces musisoli sp. nov. is proposed. The type strain is CH5-8<sup>T</sup> (=TBRC 9950<sup>T</sup>=NBRC 113997<sup>T</sup>).
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    Streptomyces salinarius sp. nov., an actinomycete isolated from solar saltern soil
    (2023-01-01)
    Klanbut, Khanungkan
    ;
    Rattanakavil, Thitiya
    ;
    Duangupama, Thitikorn
    ;
    Suriyachadkun, Chanwit
    ;
    Herron, Paul Robert
    An actinobacterium, designated strain SS06011<sup>T</sup>, was isolated from solar saltern soil collected from Samut Sakhon province, Thailand. The taxonomic position of this strain was established using the polyphasic taxonomic approach. The strain produced grey aerial spore mass on International Streptomyces Project 2 seawater agar that differentiated into spiral spore chains with rugose-surfaced spores. Strain SS06011<sup>T</sup> was found to have ll-diaminopimelic acid in the cell peptidoglycan. Whole-cell hydrolysates contained galactose, glucose and ribose. MK-9(H<inf>6</inf> ) and MK-9(H<inf>4</inf> ) were major menaquinones. The major cellular fatty acids comprised iso-C<inf>16: 0</inf>, anteiso-C<inf>15: 0</inf> and anteiso-C<inf>17: 0</inf> . Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-glycerol and phosphatidylinositol were detected in cells. These characteristics were coincident with the typical morphological and chemotaxonomic properties of the genus Streptomyces. The taxonomic affiliation at the genus level of this strain could also be confirmed by its 16S rRNA gene sequence data. Strain SS06011<sup>T</sup> showed the highest 16S rRNA gene sequence similarity to Streptomyces ardesiacus NRRL B-1773<sup>T</sup> (99.1 %), Streptomyces coelicoflavus NBRC 15399<sup>T</sup> (99.1 %) and Streptomyces hyderabadensis OU-40<sup>T</sup> (99.1 %). Digital DNA–DNA hybridization (dDDH), average nucleotide identity-blast (ANIb) and average amino acid identity (AAI) values between strain SS06011<sup>T</sup> and its closely related type strains, S. ardesiacus NBRC 15402<sup>T</sup>, S. coe-licoflavus NBRC 15399<sup>T</sup> and S. hyderabadensis JCM 17657<sup>T</sup>, were in the range of 45.4–48.4 % (for dDDH), 90.8–91.9 % (for ANIb) and 90.8–91.7 % (for AAI), respectively, which are lower than the cut-off criteria for species delineation. The DNA G+C content of genomic DNA was 71.9 mol%. With the differences in physiological, biochemical and genotypic data, strain SS06011<sup>T</sup> could be discriminated from its closest neighbours. Thus, strain SS06011<sup>T</sup> should be recognized as representing a novel species of the genus Streptomyces, for which the name Streptomyces salinarius sp. nov. is proposed. The type strain is SS06011<sup>T</sup> (=TBRC 9951<sup>T</sup>=NBRC 113998<sup>T</sup>).
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    Pradimicin U, a promising antimicrobial agent isolated from a newly found Nonomuraea composti sp. nov
    (2024-12-01)
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    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 FMUSA5-5<sup>T</sup>. 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 FMUSA5-5<sup>T</sup> 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 FMUSA5-5<sup>T</sup> and its closest type strains of the genus Nonomuraea indicated that strain FMUSA5-5<sup>T</sup> 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 FMUSA5-5<sup>T</sup> 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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    Streptomyces acidipaludis sp. nov., an actinobacterium isolated from peat swamp forest soil
    (2022-01-01)
    Nammali, Achararak
    ;
    Duangupama, Thitikorn
    ;
    Pittayakhajonwut, Pattama
    ;
    Intaraudom, Chakapong
    ;
    Suriyachadkun, Chanwit
    An actinobacterium strain PLK6-54<sup>T</sup> was isolated from Lankwai peat swamp forest soil collected from Yala province, Thailand. Strain PLK6-54<sup>T</sup> exhibited morphological and chemotaxonomic properties described for the genus Streptomyces. It formed a spiral spore chain directly on aerial mycelium. Growth was observed between 20 and 40 °C and at pH 5–8. The maximum NaCl for growth was 2% (w/v). ll-Diaminopimelic acid, arabinose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside were detected as the phospholipids. The major menaquinones were MK-10(H<inf>2</inf>) and MK-9(H<inf>6</inf>). The major cellular fatty acids were iso-C<inf>16:0</inf>, anteiso-C<inf>15:0</inf> and iso-C<inf>14:0</inf>. 16S rRNA gene sequence data supported the assignment of strain PLK6-54<sup>T</sup> to the genus Streptomyces and showed that Streptomyces rubidus NBRC 102073<sup>T</sup> (99.0%) was the closest relative. Moreover, the average nucleotide identity-blast (85.5%) and digital DNA–DNA hybridization (30.7%) values reported between strain PLK6-54<sup>T</sup> and its closest neighbour were below the threshold values for delineation of a novel species. Strain PLK6-54<sup>T</sup> could be distinguished from related validly described Streptomyces species by several phenotypic properties. The combination of genotypic and phenotypic data indicated that strain PLK6-54<sup>T</sup> is representative of a novel species of the genus Streptomyces. The name Streptomyces acidipaludis sp. nov. is proposed for strain PLK6-54<sup>T</sup>. The type strain is PLK6-54<sup>T</sup> (=TBRC 11250<sup>T</sup>=NBRC 114297<sup>T</sup>).
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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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    Nocardia acididurans sp. Nov., an acid-tolerant actinobacterium isolated from bio-fertilizer of musa species
    (2021-01-01)
    Sirireung, Narissara
    ;
    Duangupama, Thitikorn
    ;
    Suriyachadkun, Chanwit
    ;
    Thawai, Chitti
    A novel acid-tolerant actinobacterium (strain LPG 2<sup>T</sup>), which formed fragmented substrate mycelia, was isolated from bio-fertiliser of Musa spp. collected from Lampang Province, Thailand. Its morphological and chemotaxonomic properties, e.g., the presence of mycolic acid and MK-8 (H<inf>4ω-cycl</inf> ) in the cells, showed that strain LPG 2<sup>T</sup> was a member of the genus Nocardia. 16S rRNA gene sequence analysis revealed that this strain was closely related to Nocardia otitidiscaviarum NBRC 14405<sup>T</sup> (98.7 %). The low average nucleotide identity–blast and digital DNA–DNA hybridization values (<78.6 and <24.0 %, respectively), and several phenotypic differences between strain LPG 2<sup>T</sup> and its related Nocardia type strains, indicated that the strain merits classification as representing a novel species of the genus Nocardia, for which we propose the name Nocardia acididurans sp. nov. The type strain is LPG 2<sup>T</sup> (=TBRC 11242<sup>T</sup>=NBRC 114293<sup>T</sup>).