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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
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Klanbut, Khanungkan
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Fukasem, Poowadon
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Pittayakhajonwut, Pattama
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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).
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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
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Li, Lin
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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.
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Antimalarial and antimicrobial substances from the endophytic fungus Chaetomium globosum BCC71876
(2026-01-01)
Bunbamrung, Nantiya
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Intaraudom, Chakapong
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Dramae, Aibrohim
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Boonyuen, Nattawut
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Choowong, Wilunda
Three previously undescribed compounds including 2′,3′-dihydroxy-4,5′,4″-trimethoxy-p-terphenyl (1), 5-methoxyhydroperoxycochliodinol (2), and 5-(3′,3′-dimethylallyl)indole-3-oxoacetic acid (17), along with fifteen known compounds (3–16 and 18), were isolated from the endophytic fungus, Chaetomium globosum BCC71876. The chemical structures were determined by NMR spectral information as well as the comparison with those closely related compounds reported in the literature. The compounds isolated were evaluated for biological properties including antimalarial, anti-TB, anti-plant pathogenic fungal, antibacterial, and cytotoxicity. The isolated compounds exhibited a wide range of biological activities against the tested cell lines and showed very low cytotoxicity against both cancerous (MCF-7 and NCI-H187) and non-cancerous (Vero) cells, except for compounds 5, 10, 11, 17, and 18 (IC<inf>50</inf> 0.47 − 114.8 µM). Cochliodinol (5) had the strongest antimalarial activity (IC<inf>50</inf> 4.39 µM), whereas chaetomugilin J (11) showed the strongest anti-TB activity (MIC 3.13 µg/mL).
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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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cis-Decalinoyltetramic Acid Derivatives from the Palm Fungus Leptosporella arengae TBRC-BCC32590
(2025-11-28)
Intaraudom, Chakapong
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Bunbamrung, Nantiya
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Dramae, Aibrohim
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Nithithanasilp, Sutichai
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Boonyuen, Nattawut
Twelve hitherto undescribed cis-decalinoyltetramic acid derivatives (arengasetins A – L), a unique spiro[2.4]heptendione (spiroarengarone) and two benzoquinones (arengaquinones A and B), together with the highly oxygenated polycyclic molecule, epicolactone, were isolated from the palm fungus Leptosporella arengae TBRC-BCC 32590. Chemical structures were determined by extensive analyses of 2D NMR spectroscopic data and chemical means. The absolute configuration of arengasetin A (1) was confirmed by X-ray crystallographic information, while the absolute configurations of other related compounds were corroborated by comparison of NMR spectroscopic data and chemical reactions. The isolated compounds exhibited activity against Plasmodium falciparum (K1, multidrug-resistant strain, IC<inf>50</inf> 6.42 – > 38.76 μM), Bacillus cereus (MIC 0.78 – > 50.0 μg/mL), Staphylococcus aureus (MIC 1.56 – > 50.0 μg/mL), and Mycobacterium tuberculosis (MIC 6.25 – > 50.0 μg/mL). Cytotoxicity against both cancerous (MCF-7 and NCI-H187) and noncancerous (Vero) was also reported.
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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
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Pansomsuay, Rawirat
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Thanaboripat, Dusanee
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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
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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).
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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
;
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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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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