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Fitoterapia Mar 2024Actinomadura sp., which is usually found in muddy habitats, produces various secondary metabolites with biological activities. In this study, five new compounds named...
Actinomadura sp., which is usually found in muddy habitats, produces various secondary metabolites with biological activities. In this study, five new compounds named formosensin A (1), formosensin B (2), oxanthroquinone-3-O-α-d-mannose (8), oxanthromicin A (9), and oxanthromicin B (10) were isolated from the culture of Actinomadura sp. together with five known compounds (3-7). Their structures were elucidated by extensive spectroscopic methods including NMR and MS. In particular, the absolute configurations of compounds 1 and 2 were determined using computational methods. Moreover, compounds 1-2 and 8-10 were screened for cytotoxic activity using a panel of human tumor cell lines. Compound 9 induced significant cytotoxicity in five human tumor cell lines (HL-60, A-549, SMMC-7721, MCF-7, and SW480) with IC values of 8.7, 17.5, 15.0, 17.8, and 14.6 μM, respectively. These findings suggested that compound 9 could provide therapeutic benefits in the treatment of tumor-related diseases.
Topics: Humans; Actinomadura; Molecular Structure; Antineoplastic Agents; Cell Line, Tumor; Anthraquinones
PubMed: 38181893
DOI: 10.1016/j.fitote.2023.105806 -
New Microbes and New Infections Nov 2021Two hundred and eighty-six isolates from human clinical samples were identified between 1996 and 2019 as belonging to 8 families, 19 genera and 88 species of . The most...
Two hundred and eighty-six isolates from human clinical samples were identified between 1996 and 2019 as belonging to 8 families, 19 genera and 88 species of . The most identified genera were (182 strains from 45 species), (29 strains, 5 species), (21 strains, 6 species) and (18 strains, 5 species). The rest of the identified genera (15) contained 27 species with 36 isolates. Of the species studied, only 13/88 had been documented previously as isolates from clinical samples, and in some cases, as true pathogens. In this sense, a literature review of the species found in infections or in clinical samples without clear involvement in pathology has been carried out. Finally, the susceptibility to 8 antimicrobial agents has been studied. showed high resistance (80.8%) against cefotaxime and cotrimoxazole (55.5%), and no isolate resistance to amikacin and linezolid have been found. Lower percentages of resistance have been found in other genera, except in (100% against cotrimoxazole and 44.4% against erythromycin). The greatest resistance in these genera was to cotrimoxazole (29.8) and erythromycin (27,9%), and no resistance to linezolid has been found in these genera. In , no resistant isolates have been found against any antibiotic studied. Only 3/104 isolates were resistant to amikacin in , , and One isolate of was resistant to imipenem.
PubMed: 34917388
DOI: 10.1016/j.nmni.2021.100946 -
International Journal of Systematic and... Dec 2021An actinomycete strain, LCR2-06, isolated from a lichen sample on rock collected from Chiang Rai Province (Pong Phra Bat Waterfall), Thailand, was characterized using a...
An actinomycete strain, LCR2-06, isolated from a lichen sample on rock collected from Chiang Rai Province (Pong Phra Bat Waterfall), Thailand, was characterized using a polyphasic approach. The strain grew at 25-45 °C, pH 6-11 and on International Project 2 agar plate with 5 % (w/v) NaCl. It contained -diaminopimelic acid as the diamino acid in whole-cell hydrolysates. Rhamnose, ribose, xylose, madurose, glucose and galactose were detected as whole-cell sugar hydrolysates. Mycolic acids were absent. The -acyl type of muramic acid was acetyl. The strain contained C, TBSA 10-methyl C and 2-hydroxy C as the predominant fatty acids and MK-9(H), MK-9(H) and MK-9(H) as the major menaquinones. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The draft genome of strain LCR2-06 was closely related to TBRC 7225 (99.2 %), NBRC 15918 (98.8 %), TISTR 2400 (98.5 %) and JCM 33455 (97.9 %). The draft genome of LCR2-06 was 11.1 Mb with 10 588 coding sequences with an average G+C content of 72.7 mol%. Results of genomic analysis revealed that the ANIb and ANIm values between strain LCR2-06 and TISTR 2400 were 90.0 and 92.0 %, respectively. The digital DNA-DNA hybridization value was 43.9 % in comparison with the draft genome of TISTR 2400. The strain produced an antibacterial compound active against ATCC 6633 and ATCC 9341. The results of taxonomic analysis suggested that strain LCR2-06 represented a novel species of the genus for which the name sp. nov. is proposed. The type strain is LCR2-06 (=JCM 33065=KCTC 49547=NBRC 114810=LMG 32136=TISTR 2935).
Topics: Actinomadura; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lichens; Nucleic Acid Hybridization; Oligopeptides; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Thailand; Vitamin K 2
PubMed: 34870574
DOI: 10.1099/ijsem.0.005126 -
International Journal of Systematic and... Aug 2020The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was...
The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus and it was most closely related to DSM 45347 (99.31 % similarity) and DSM 44485 (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained -2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H), with minor amounts of MK-9(H) and MK-9(H). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of Cω9, Cω7 and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NRRL B-65521(=LMG 31258=DSM 109019).
Topics: Actinobacteria; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Thailand; Vitamin K 2
PubMed: 32701429
DOI: 10.1099/ijsem.0.004348 -
Microbial Ecology Nov 2023Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing...
The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.
Topics: Ecosystem; Rhizosphere; Bacteria; Proteobacteria; Acidobacteria; Fabaceae; Soil; Plants; Nitrogen; Soil Microbiology
PubMed: 38008827
DOI: 10.1007/s00248-023-02320-9 -
Applied and Environmental Microbiology May 2022Nonheme iron- and α-ketoglutarate (αKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C()-H bonds,...
Nonheme iron- and α-ketoglutarate (αKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C()-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/Fe/Cl and AdeV/Fe/Cl/αKG at resolutions of 1.76 and 1.74 Å, respectively. AdeV possesses a typical β-sandwich topology with H194, H252, αKG, chloride, and one water molecule coordinating Fe in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and α-ketoglutarate (αKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/Fe/Cl and AdeV/Fe/Cl/αKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides.
Topics: Carrier Proteins; Ferrous Compounds; Halogenation; Halogens; Iron; Ketoglutaric Acids; Molecular Docking Simulation; Nucleotides
PubMed: 35435717
DOI: 10.1128/aem.02497-21 -
The Journal of Antibiotics Oct 2022Nine new hydroxyphenyloxazolines, madurastatin B4, C2, D3 and D4, E1 and E2, F1 as well as G1 and G2 (8-16), along with two new enantiomers of madurastatin D1 (ent-6)...
Nine new hydroxyphenyloxazolines, madurastatin B4, C2, D3 and D4, E1 and E2, F1 as well as G1 and G2 (8-16), along with two new enantiomers of madurastatin D1 (ent-6) and D2 (ent-7) and two known congeners, madurastatin B1 (2) and C1 (5), were isolated from the liquid culture of Actinomadura sp. ST100801 based on the initial activity against Escherichia coli screened in bicarbonate-supplemented Mueller Hinton II medium and identification via molecular networking. Structure elucidation was achieved by comprehensive 1D and 2D NMR as well as MS/MS fragmentation analyses. Their absolute configuration was determined by Marfey's analysis. Complemented with functionalized hydroxyphenyloxazolines (2, 4, 17-18) obtained by total synthesis, the isolated compounds were evaluated for antibacterial activities revealing MICs down to 4 µg ml against Moraxella catarrhalis. Therefore, this study enlarges the family of madurastatin siderophores.
Topics: Actinomadura; Anti-Bacterial Agents; Escherichia coli; Microbial Sensitivity Tests; Molecular Structure; Siderophores; Tandem Mass Spectrometry
PubMed: 36056265
DOI: 10.1038/s41429-022-00557-z -
Indian Journal of Dermatology,... 2022Background Mycetoma is widespread in Yemen; however, there are only a few documented reports on the entity from this geographical area. Methods A prospective study of...
Background Mycetoma is widespread in Yemen; however, there are only a few documented reports on the entity from this geographical area. Methods A prospective study of 184 cases of mycetoma (male 145 and female 39) from different regions of north-western Yemen was conducted between July 2000 and May 2014. Clinical profile was recorded in a standardized protocol. The diagnosis was based on clinical features, X-ray studies, examination of grains, and histopathology. Results Eumycetoma was diagnosed in 129, caused by Madurella mycetomatis in 124, Leptosphaeria senegalensis in one and pale grain fungus in four, whereas actinomycetoma occurred in 55, caused by Streptomyces somaliensis in 29, Actinomadura madurai in nine, Actinomadura pelletieri in one, and Nocardia in sixteen. Eumycetoma cases were treated with prolonged course of antifungal drugs, mostly ketoconazole, with itraconazole being used in four patients, along with excision or debulking. Results were better when antifungal drugs were given two to three months before surgery and in those who received itraconazole. Actinomycetoma cases were initially treated with co-trimoxazole monotherapy; later streptomycin was added in 30 cases. Six patients who did not show adequate improvement and two others from the start were treated with modified Welsh regimen and with good results. Limitations Identification of different causative agents was done by histopathology and could not be reconfirmed by culture. Conclusion Mycetoma is widespread in north-western Yemen with a higher incidence of eumycetoma and a majority of the cases were caused by Madurella mycetomatis. Modified Welsh regimen in actinomycetoma and itraconazole with excision in eumycetoma showed the best results.
Topics: Antifungal Agents; Female; Humans; India; Itraconazole; Madurella; Male; Mycetoma; Prospective Studies; Yemen
PubMed: 35389029
DOI: 10.25259/IJDVL_500_2021 -
International Journal of... 2023The PAH degrading microbial consortium was collected from sodic soil of the nursery of Guru Jambheshwar University of Science and Technology, Hisar, Haryana (India). And...
The PAH degrading microbial consortium was collected from sodic soil of the nursery of Guru Jambheshwar University of Science and Technology, Hisar, Haryana (India). And the soil was artificially amended with phenanthrene and naphthalene to isolate the PAHs degrading microbial consortium. The diversity of microbial consortium was analyzed using the NGS (Next Generation Sequencing) based metagenomic approach. The result of diversity analysis showed species were present in the consortium. Moreover, Sphingomonas, Arthrobacter, Sphingobium, Azospirillium, Thirohodococcus, and Pelotomaculum were the prominent pollutant degrader genera in the microbial consortium. Since the bioremediation of these pollutants occurs with a significant reduction in toxicity, the study's perspective is to use this type of consortium for bioremediation of specifically contaminated soil.
Topics: Biodegradation, Environmental; Soil; Polycyclic Aromatic Hydrocarbons; Microbiota; Microbial Consortia; Soil Pollutants; Soil Microbiology
PubMed: 36694290
DOI: 10.1080/15226514.2023.2170321 -
International Journal of Systematic and... Oct 2019The taxonomic position of '' LMG 30035, a semduramicin-producing mutant of strain ATCC 53666, which was isolated from a soil sample collected in Yamae Village, Kamamoto,...
The taxonomic position of '' LMG 30035, a semduramicin-producing mutant of strain ATCC 53666, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035 was found to be closely related to the type strains of ATCC 49459 (98.88 %) and JCM 7474 (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035 represents a novel species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named species). Analysis of the cell wall revealed the presence of -diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H), MK-9(H), MK-9(H) and MK-9(H). The major fatty acids were C, 10-methyl C, C and C. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035 from validly named species of the genus , and therefore, we propose to classify this strain formally as the novel species sp. nov. with LMG 30035 (=CECT 9808,=ATCC 53664) as the type strain.
Topics: Actinobacteria; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Ionophores; Japan; Nigericin; Nucleic Acid Hybridization; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 31310199
DOI: 10.1099/ijsem.0.003591