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Streptomyces tyrfis sp. nov., an actinobacterium isolated from Thai peat swamp forest soil and its promising secondary metabolites
(2026-12-01)
Kottip, Penkawee
;
Klanbut, Khanungkan
;
Fukasem, Poowadon
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Pittayakhajonwut, Pattama
;
Intaraudom, Chakapong
An actinomycete strain, PTD5-9T, was isolated from peat swamp forest soil in Narathiwat Province, Thailand. Chemotaxonomic features and phylogenetic analysis based on the 16S rRNA gene sequence placed this strain within the genus Streptomyces. It exhibited the highest sequence similarity to Streptomyces gelaticus NRRL B-2928ᵀ (99.38%) and Streptomyces sanglieri NBRC 100784ᵀ (99.31%). However, the average nucleotide identity based on MUMmer (ANIm) values (88.48–88.56%), the average amino acid identity (84.37–84.97%), and digital DNA–DNA hybridization (dDDH) estimates (31.2–36.5%) were significantly below the accepted thresholds for species demarcation, supporting its classification as a new species within the genus. Accordingly, the name Streptomyces tyrfis sp. nov. is proposed. The crude extract derived from the culture broth of strain PTD5-9ᵀ exhibited potent antibacterial activity against Gram-positive bacteria (MIC ≤ 250 µg/mL). Subsequent chemical analysis led to the identification of ten bioactive secondary metabolites: isocycloheximide (1), (2R,4S,6E)-anhydrocycloheximide (2), actiphenol (3), (−)-phenatic acid A (4), 8-O-methyltetrangomycin (5), 8-O-methylrabelomycin (6), 4-hydroxy-8-O-methylrabelomycin (7), tetrangulol methyl ether (also known as X-14881 E) (8), (−)-elmonin (9), and 2-phenylacetamide (10). Among these, compounds 3, 6, 7, and 8, which were isolated in sufficient quantities, exhibited notable inhibitory activity against Mycobacterium tuberculosis, with MIC values ranging from 3.13 to 25.0 µg/mL. Furthermore, compounds 6, 7, and 8 demonstrated pronounced cytotoxicity against human small cell lung cancer (NCI-H187) cells (IC₅₀: 1.10–7.80 µM), and against human breast cancer (MCF-7) cells (IC₅₀: 1.21–24.6 µM).
4
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The phytohormone indole-3-acetic acid induces quorum sensing signal DSF turnover via a positive feedback biosynthetic loop in the phytopathogen Xanthomonas campestris
(2026-12-01)
Li, Si Nan
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Zhang, Ming Lei
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Cui, Ying
;
Li, Lin
;
Thawai, Chitti
Indole-3-acetic acid (IAA) accumulates in host plants following infection by Xanthomonas campestris pv. campestris (Xcc), the causal agent of cruciferous black rot. How exposure to IAA affects the invading Xcc remains unclear. Here, we demonstrate that either exogenous addition of IAA or endogenous production of IAA induced turnover of the quorum sensing (QS) signal diffusible signaling factor (DSF) in a RpfB-dependent manner. IAA addition prevented the cytoplasmic and culture pH decline. Transcriptomic analyses revealed four IAA-regulated gene clusters. Specifically, IAA induced the expression of trpB-A, enhancing tryptophan biosynthesis and intracellular IAA accumulation, and thereby establishing a self-reinforcing synthesis loop. IAA upregulated F<inf>0</inf>F<inf>1</inf> ATP synthases and a resistance-nodulation-cell division (RND)-family efflux pump HepABCD to induce a pH-dependent DSF turnover. Moreover, IAA downregulated another RND family efflux pump IaepABCDE to induce a pH-independent DSF turnover. Finally, the IAA-regulated gene clusters were transcribed during the XC1 infection of cabbage. Collectively, these findings reveal a previously unrecognized role of IAA in modulating bacterial QS, underscoring the importance of IAA in the molecular dialogue between the pathogen and its host.
2
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Discovery of Streptomyces marinisediminis sp. nov., a new thiolutin producing actinomycete isolated from Thai marine sediment
(2025-12-01)
Pansomsuay, Rawirat
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Fukasem, Poowadon
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Pittayakhajonwut, Pattama
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Intaraudom, Chakapong
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Suriyachadkun, Chanwit
Thiolutin and 2,2-dioxidothiolutin are sulfur-containing antibiotics discovered through a targeted high-throughput screening strategy designed to identify compounds with antimicrobial activity. The producing strain, JHD1T, is an actinomycete isolated from marine sediment collected in Chonburi Province, Thailand. Chemotaxonomic characteristics and 16S rRNA gene sequence analysis indicated that strain JHD1T belongs to the genus Streptomyces. Taxonomic analysis using a polyphasic approach further supported its placement within the genus Streptomyces. The strain exhibited low similarity to its closest known relatives, Streptomyces alkaliterrae OF1T and Streptomyces chumphonensis KK1-2T, with average nucleotide identity based on MuMmer ultra-rapid aligning tool (ANIm) values of 85.7–86.2%, average amino acid identity (AAI) values of 71.8–78.1%, and digital DNA–DNA hybridization (dDDH) values of 23.4–25.0%, all well below the established thresholds for species delineation. These results reveal that strain JHD1T represents a novel species within the genus Streptomyces, for which the name Streptomyces marinisediminis sp. nov. is proposed. The crude extract obtained from the culture broth of strain JHD1T exhibited strong antimicrobial activity against Gram-positive bacteria and led to the discovery of two promising secondary metabolites, thiolutin and 2,2-dioxidothiolutin, along with 8-amino-2H-benz[e][1,3]oxazine-2,4(3H)-dione, benadrostin, 2,3-dihydroxybenzamide, and 2-hydroxy-3-methoxybenzamide. In this study, 2,2-dioxidothiolutin was structurally confirmed for the first time by X-ray crystallographic analysis. Interestingly, thiolutin demonstrated strong anti-human small cell lung cancer (NCI-H187) activity, with an IC₅₀ value of 0.35 µg/mL, and also showed cytotoxicity against human breast cancer (MCF-7) cells, with an IC₅₀ value of 5.61 µg/mL.
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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
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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).
2
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Host plant-derived benzoic acid interferes with 4-hydroxybenzoic acid degradation in the phytopathogen Xanthomonas campestris by competitively binding to PobR
(2024-12-01)
Chen, Bo
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Zhou, Lian
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Song, Kai
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Thawai, Chitti
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He, Ya Wen
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot in Brassica vegetables, which can induce the host plant to produce salicylic acid and 4-hydroxybenzoic acid (4-HBA) during infection. Xcc was previously shown to sense and degrade host plant-derived 4-HBA via the sensor PobR and a PobA-dependent pathway. The degradation of 4-HBA is associated with Xcc virulence in cabbage. The present study generated a reporter strain XC1
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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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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.
1
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Fructose promotes pyoluteorin biosynthesis via the CbrAB-CrcZ-Hfq/Crc pathway in the biocontrol strain Pseudomonas PA1201
(2023-12-01)
Cui, Ying
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Song, Kai
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Jin, Zi Jing
;
Lee, Learn Han
;
Thawai, Chitti
Biocontrol strain Pseudomonas PA1201 produces pyoluteorin (Plt), which is an antimicrobial secondary metabolite. Plt represents a promising candidate pesticide due to its broad-spectrum antifungal and antibacterial activity. Although PA1201 contains a complete genetic cluster for Plt biosynthesis, it fails to produce detectable level of Plt when grown in media typically used for Pseudomonas strains. In this study, minimum medium (MM) was found to favor Plt biosynthesis. Using the medium M, which contains all the salts of MM medium except for mannitol, as a basal medium, we compared 10 carbon sources for their ability to promote Plt biosynthesis. Fructose, mannitol, and glycerol promoted Plt biosynthesis, with fructose being the most effective carbon source. Glucose or succinic acid had no significant effect on Plt biosynthesis, but effectively antagonized fructose-dependent synthesis of Plt. Promoter-lacZ fusion reporter strains demonstrated that fructose acted through activation of the pltLABCDEFG (pltL) operon but had no effect on other genes of plt gene cluster; glucose or succinic acid antagonized fructose-dependent pltL induction. Mechanistically, fructose-mediated Plt synthesis involved carbon catabolism repression. The two-component system CbrA/CbrB and small RNA catabolite repression control Z (crcZ) were essential for fructose-induced Plt synthesis. The small RNA binding protein Hfq and Crc negatively regulated fructose-induced Plt. Taken together, this study provides a new model of fructose-dependent Plt production in PA1201 that can help improve Plt yield by biosynthetic approaches.
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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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