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A novel Streptomyces strain, designated 3_2 T , was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2 T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2 T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2 T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2 T , compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2 T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2 T possessed MK-9 (H 6 ) and MK-9 (H 8 ) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C 16:0 (23.6%) and anteiso-C 15:0 (10.4%). The fermentation products of strain 3_2 T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2 T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2 T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2 T (= JCM 34935 T  = GDMCC 4.217 T )., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Background: New antibiotics are urgently needed in clinical treatment of superdrug-resistant bacteria. Nonribosomal peptides (NRPs) are a major source of antibiotics because they exhibit structural diversity, and unique antibacterial mechanisms and resistance. Analysis of gene clusters of S. agglomeratus 5-1-3 showed that Clusters 3, 6, 12, 21, and 28 were used to synthesize NRPs. Here, we examined secondary metabolites of S. agglomeratus 5-1-3 isolated from soils in the Qinghai-Tibet Plateau, China, for NRPs with antibacterial activity., Results: We isolated a total of 36 Streptomyces strains with distinct colony morphological characteristics from 7 soil samples. We screened 8 Streptomyces strains resistant to methicillin-resistant Staphylococcus aureus (MRSA). We then selected S. agglomeratus 5-1-3 for further study based on results of an antibacterial activity test. Here, we isolated three compounds from S. agglomeratus 5-1-3 and characterized their properties. The crude extract was extracted with ethyl acetate and purified with column chromatography and semipreparative high-performance liquid chromatography (HPLC). We characterized the three compounds using NMR analyses as echinomycin (1), 5,7,4'-trihydroxy-3.3',5'-trimethoxy flavone (2), and 2,6,2', 6'-tetramethoxy-4,4-bis(2,3-epoxy-1-hydroxypropyl)-biphenyl (3). We tested the antibacterial activity of pure compounds from strain 5-1-3 with the Oxford cup method. NRP echinomycin (1) showed excellent anti-MRSA activity with a minimum inhibitory concentration (MIC) of 2.0 μg/mL. Meanwhile, MIC of compound 2 and 3 was 128.0 μg/mL for both. In addition, 203 mg of echinomycin was isolated from 10 L of the crude extract broth of strain 5-1-3., Conclusion: In this study, S. agglomeratus 5-1-3 with strong resistance to MRSA was isolated from the soils in the Qinghai-Tibet Plateau. Strain 5-1-3 had a high yield of echinomycin (1) an NRP with a MIC of 2 μg/mL against MRSA. We propose that echinomycin derived from S. agglomeratus 5-1-3 may be a potent antibacterial agent for pharmaceutical use., (© 2023. The Author(s).)

We report the discovery and functional characterization of a new bacterial tRNA species. The tRNA-Asp-AUC, from a fast-growing desert streptomycete, decodes GAU codons. In the absence of queuosine tRNA anticodon modification in streptomycetes, the new tRNA circumvents inefficient wobble base-pairing during translation. The tRNA, which is constitutively expressed, greatly enhances synthesis of 4 different antibiotics in the model mesophilic species Streptomyces coelicolor, including the product of a so-called cryptic pathway, and increases yields of medically-important antibiotics in other species. This can be rationalised due to increased expression of both pleiotropic and pathway-specific transcriptional activators of antibiotic biosynthesis whose genes generally possess one or more GAT codons; the frequency of this codon in these gene sets is significantly higher than the average for streptomycete genes. In addition, the tRNA enhances production of cobalamin, a precursor of S-adenosyl methionine, itself an essential cofactor for synthesis of many antibiotics. The results establish a new paradigm of inefficient wobble base-pairing involving GAU codons as an evolved strategy to regulate gene expression and, in particular, antibiotic biosynthesis. Circumventing this by expression of the new cognate tRNA offers a generic strategy to increase antibiotic yields and to expand the repertoire of much-needed new bioactive metabolites produced by these valuable bacteria., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

A novel actinobacterial strain, designated Z022 T , isolated from a soil sample collected from Dangxiong in Tibet Autonomous Region (PR China), was determined by polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces. Strain Z022 T showed high similarity value to Streptomyces lucensis NBRC 13056 T (98.87 %) and S. achromogenes subsp . achromogenes NBRC 12735 T (98.68 %) based on the 16S rRNA gene phylogenetic tree. The genomic DNA G+C content of strain Z022 T based on the genome sequence was 72.16 mol%. DNA-DNA relatedness values between strain Z022 T and strain Streptomyces lucensis NBRC 13056 T was 23.7±1.3 % and significantly lower than 70 %. Chemotaxonomic data revealed that strain Z022 T possessed MK-9(H 8 ) and MK-9(H 6 ) as the predominant menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose, xylose and ribose as whole cell sugars. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the predominant polar lipids; anteiso-C 15 : 0 , iso-C 16 : 0 , and anteiso-C 17 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z022 T (=JCM 31053 T =CGMCC 4.7273 T ) should be classified in the genus Streptomyces as Streptomyces dangxiongensis sp. nov.

A novel actinobacterial strain, designated S10 T , was isolated from a sand sample collected from the Qaidam Basin in Qinghai province, China. The strain S10 T exhibited antibacterial activity against MRSA. The taxonomic position of the strain S10 T was determined by a polyphasic approach. There were six copies of 16S rDNA in S10 T which were not same exactly (MH257693-MH257698). Phylogenetic analysis of 16S rRNA gene sequences indicated the strain belonging to the genus Streptomyces and it showed high sequence similarities with Streptomyces chartreusis NBRC 12753 T (99.31%), Streptomyces phaeoluteigriseus DSM 41896 T (99.24%), Streptomyces variegatus NRRL B-16380 T (99.17%) and Streptomyces flavovariabilis NRRL B-16367 T (99.17%) comparing with MH257693, MH257695, MH257696, MH257697, and MH257698. Similarities with Streptomyces kunmingensis NBRC14463 T (98.82%), Streptomyces bungoensis DSM 41781 T (98.76%), S. chartreusis NBRC 12753 T (98.69%) and S. phaeoluteigriseus DSM 41896 T (98.62%) with MH257694. Whole-genome average nucleotide identity (ANI) values between strain S10 T and S. chartreusis NBRC 12753 T , S. phaeoluteigriseus DSM 41896 T , S. variegatus NRRL B-16380T, S. flavovariabilis NRRL B-16367 T , S. kunmingensis NBRC 14463 T , S. bungoensis DSM 41781 T were 83.63%, 82.89%, 92.55%, 92.51%, 79.29, and 82.87%, respectively, suggesting that the strain S10 T represented a new species. A phylogenetic analysis comparing the S10 T genome with those of 336 other sequenced Streptomyces genomes confirmed its relatedness with Streptomyces variegatus NRRL B-16380 T and Streptomyces flavovariabilis NRRL B-16367 T . Strain S10 T contained LL-diaminopimelic acid in the cell wall. The predominant menaquinones were MK-9(H 6 ) and MK-9(H 8 ) and the major fatty acids were iso-C 15:0, anteiso-C 15:0 , iso-C 16:0 , and anteiso-C 17:0 . Phospholipids detected were diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline, three unknown phospholipids, an unknown aminophospholipid and an unknown phosphatidyl glycolipid. On the basis of these genotypic and phenotypic data, it is proposed that isolate S10 T (=JCM 31184 T =CGMCC 4.7315 T ) should be classified in the genus Streptomyces as Streptomyces qaidamensis sp. nov.

A novel actinobacterial strain, designated Z1027T, was isolated from a soil sample collected near the Tuotuo River, Qinghai-Tibet Plateau (China). The strain exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus. The taxonomic position of strain Z1027T was determined using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree, together with Streptomyces turgidiscabies ATCC 700248T (99.19 % similarity), Streptomyces graminilatus JL-6T (98.84 %) and Streptomyces reticuliscabiei CFBP 4531T (98.36 %). The genomic DNA G+C content of strain Z1027T was 74±1 mol%. The DNA-DNA relatedness values between strain Z1027T and Streptomyces turgidiscabies ATCC 700248T and Streptomyces reticuliscabiei CFBP 4531T were 38.5±0.4 and 26.2±1.2 %, respectively, both of them significantly lower than 70 %. Chemotaxonomic data revealed that strain Z1027T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, ll-diaminopimelic acid as the diagnostic diamino acid and galactose as a whole-cell sugar. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatydilinositol and seven other unknown polar lipids were detected; iso-C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1027T (=CGMCC 4.7272T=JCM 31054T) should be classified as the type strain of a novel species of the genus Streptomyces,Streptomyces lacrimifluminis sp. nov.