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Characterization, comparative genomics, and metabolome analysis of Streptomyces tuberiscabiei sp. nov., a novel actinomycete causing potato scab disease in Long Khot, Chiang Mai Province, Thailand
(2026-07-01)
Inthong, Tanchanok
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Wannawong, Thippawan
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Mhuantong, Wuttichai
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Hongprasit, Aphinan
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Tanasupawat, Somboon
Three actinomycete strains, WSLK1–3T, WSLK1–4, and WSLK1–5, associated with scabby potato tuber, were characterized using polyphasic and genome-based taxonomy. All strains were found to be Gram-stain-positive, filamentous bacteria, including LL-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, mannose, rhamnose, and ribose. MK-9(H<inf>6</inf>) and MK-9(H<inf>10</inf>) were major menaquinones; C<inf>16:0</inf>, isoC<inf>16:0</inf>, ante iso-C<inf>15:0</inf>, and anteiso -C<inf>17:0</inf> were major cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol mannoside were major phospholipids; and DNA G + C contents were 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strains WSLK1–3T, WSLK1–4, and WSLK1–5 are closely related to Streptomyces canus DSM 40017T (=JCM 4212T), and S. pseudovenezuelae DSM 40212T (=JCM 11516T), respectively. The 16S rRNA gene sequences, average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm), and digital DNA-DNA hybridization (dDDH) values among the three strains were 100%, 99.12%, 99.33%, and 94.3%, respectively, indicating that these strains belong to the same species. Strains WSLK1–3T, WSLK1–4, and WSLK1–5 showed 88.54–90.62% ANIb, 90.99–92.27% ANIm, and 40.4–45.1% to their closely related type strains: S. canus JCM 4212T, and S. pseudovenezuelae JCM 11516T. All novel strains were pathogenic, causing necrosis on potato tuber slices, inhibiting plant seedlings, and inducing superficial to raised scab lesions on potato tubers. Based on the phenotypic, chemotaxonomic, pathogenic, and genomic data, strains WSLK1–3T, WSLK1–4, and WSLK1–5 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces tuberiscabiei sp. nov. is proposed. The type strain is WSLK1–3T (=TBRC 19150T = LMG 33893T).
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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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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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Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers
(2024-01-01)
Wannawong, Thippawan
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Mhuantong, Wuttichai
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Macharoen, Pipat
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Niemhom, Nantawan
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Sitdhipol, Jaruwan
A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H<inf>6</inf>) was the predominant menaquinone, whereas iso-C<inf>16:0</inf> and iso-C<inf>15:0</inf> were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.
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Antimalarial and antimicrobial substances isolated from the endophytic actinomycete, Streptomyces aculeolatus MS1-6
(2023-03-01)
Kuncharoen, Nattakorn
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Bunbamrung, Nantiya
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Intaraudom, Chakapong
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Choowong, Wilunda
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Thawai, Chitti
Seven undescribed compounds, including four naphthoquinone terpenoids (aculeolatins A – D), one rare 2-nitropyrrole terpenoid (nitropyrrolin F), and two hydroxamate siderophores (aculeolamides A and B) and one further undescribed compound (2,5,7-trihydroxy-3,6-dimethylnaphthalene-1,4-dione), together with eleven known compounds (arromycin, phenaziterpene A, nitropyrrolin A, heronapyrroles A and B, salaceyin A, 5,7-dihydroxy-2-isopropylchromone, 1-hydroxyphenazine, 1-methoxyphenazine, 1-acetyl-β-carboline, and N-(2-phenylethyl) acetamide), were isolated from the cultures of the endophytic Streptomyces aculeolatus MS1-6. The structures of the isolated compounds were determined using NMR spectroscopy and corroborated using chemical modification. These compounds exhibited a broad spectrum of biological activities, including antimalarial (IC<inf>50</inf> 6.03–9.84 μg/mL), antitubercular (MIC 3.13–6.25 μg/mL), anti-plant pathogenic fungal (MIC 25.0–50.0 μg/mL), and antibacterial (MIC 3.03–50 μg/mL) activities; however, they displayed unremarkable cytotoxicity against cancerous (MCF-7 and NCI–H187) and non-cancerous (Vero) cell lines.
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Antibacterial activity of thai medicinal plant extracts against oral and gastrointestinal pathogenic bacteria and prebiotic effect on the growth of lactobacillus acidophilus
(2018-01-01)
Nanasombat, Suree
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Kuncharoen, Nattakorn
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Ritcharoon, Benjarat
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Sukcharoen, Paweena
The 25 crude methanolic extracts of Thai medicinal plants were tested for their antibacterial activity against 10 bacterial strains using disk diffusion assay and minimum inhibitory concentration (MIC) determination. Rhubarb (Rheum palmatum) root, wild turmeric (Curcuma aromatica) rhizome, aleppo oak (Quercus infectoria) gall and ringworm bush (Cassia alata) stem extracts possessed strong antibacterial activity. Aleppo oak and wild turmeric extracts strongly inhibited Y. enterocolitica growth, while aromatic ginger (Kaempferia galanga) rhizome, rhubarb, wild turmeric and ringworm bush extracts strongly inhibited the growth of Porphyromonas gingivalis, an oral pathogen (0.32 mg/mL MIC). The aleppo oak gall extract had the highest phenolics and tannins (672.13 mg gallic acid equivalents (GAE)/g extract and 884.79 mg tannic acid equivalents (TAE)/g extract, respectively), whereas copper pod (Peltophorum pterocarpum) stem bark extract had the highest flavonoids (5,293.60 mg quercetin eqivalents (QE)/g extract). Five plant extracts with high water soluble carbohydrate were tested for their prebiotic properties. Their indigestible polysaccharide contents and prebiotic effect on the growth of Lactobacillus acidophilus in MRS broth were determined. Of all, mangosteen (Garcinia mangostana) fruit peel, nutgrass (Cyperus rotundus) rhizome and gac (Momordica cochinchinensis) root extracts had high indigestible polysaccharide contents, and exhibited good stimulating effect to the growth of L. acidophilus.
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