Streptomyces sediminis sp. nov. isolated from crater lake sediment

Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis

During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2 Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

Streptomyces polyasparticus sp. nov. isolated from cotton field soil by a medium applied with polyaspartic acid

A novel Streptomyces strain (TRM66268-LWL^T) was isolated from cotton field soil by a medium supplied with polyaspartic acid (PASP) at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. The strain was found to degrade PASP, and grow well on the medium to take PASP as the sole carbon source. The TRM66268-LWL^T fermentation broth was applied to the surface of PASP, and there were pores on the surface of PASP after a period of time. The strain was observed to be Gram-stain-positive and to form greyish-white aerial mycelia that differentiated into straight spore chains with round spores. The whole-cell sugar pattern of TRM 66268-LWL^T consisted of ribose, mannose and arabinose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside, phosphatidylinositol and two undetermined polar lipids. The predominant menaquinones were MK-7, MK-7(H₄), MK-9(H₈), MK-10(H₆). The diagnostic cell wall amino acid was identified as LL-diaminopimelic acid. The G+C content of strain TRM66268-LWL^T was 70.11 mol%. The average nucleotide identity value between strain TRM66268-LWL^T and the phylogenetically related strain Streptomyces indicus IH32-1^T was calculated to be 85.49%. The digital DNA-DNA hybridization value between them was 30.40%. A multilocus sequence analysis of five house-keeping genes (atpD, gyrB, rpoB, recA and trpB) also illustrated that strain TRM66268-LWL^T should be assigned to the genus Streptomyces. On the basis of evidence from polyphasic study, strain TRM66268-LWL^T is designated as representing a novel species of the genus Streptomyces, for which the name Streptomyces polyasparticus sp. nov. is proposed. The type strain is TRM66268-LWL^T (CCTCC AA 2020003^T = LMG32106^T).

Streptomyces coryli sp. nov., isolated from hazelnut orchard soil

A novel actinobacteria, isolate A7024T, was isolated from commercial hazelnut orchard soil sample which was collected at Duzce, West Black Sea region, Turkey. A polyphasic taxonomic study was carried out to determine the status of this isolate. The phylogenetic tree reconstructed using the neighbour-joining algorithm based on 16S rRNA gene sequences indicated that isolate A7024T was positioned within the members of the genus Streptomyces with the highest sequence similarity (97.7 %) to Streptomyces cadmiisoli ZFG47T. The organism formed an extensively branched substrate and aerial hyphae which generated irregular rod-shaped spores with smooth-surfaces. The cell wall of strain A7024T contained ll-diaminopimelic. Glucose, mannose and ribose were detected as whole-cell sugars. Its polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and three unidentified glycolipids. Major menaquinones were MK-9(H6) and MK-9(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Strain A7024T had a genome size of 9.0 Mb with a genome G+C content of 71.5 mol%. The low level of 16S rRNA gene similarity, 19.3 ± 2.3% digital DNA–DNA hybridization and 76.94 % average nucleotide identity values, as well as some different phenotypic characteristics allowed the strain to be distinguished from the closely related type strains. Therefore, it is concluded that strain A7024T represents a novel species of the genus of Streptomyces , for which the name Streptomyces coryli sp. nov. is proposed. The type strain is A7024T (=DSM 42066T=KCTC 29102T=NRRL B-24888T).

Streptomyces boluensis sp. nov., isolated from lake sediment

A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain YC537^T, was isolated from lake sediment collected from Yenicaga Lake, Bolu, Turkey, and subjected to a polyphasic taxonomic approach. The organism had phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis of strain YC537^T showed that it is closely related to the type strain of Streptomyces ziwulingensis F22^T (97.9% sequence similarity), Streptomyces tauricus JCM 4837 ^T (97.7%) and Streptomyces beijiangensis NBRC 100044 ^T (97.6%). The cell wall of the strain contained LL-diaminopimelic acid and the cell-wall sugars were glucose, galactose and ribose. The major phospholipids of strain YC537^T were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H₆) and MK-9(H₈). The major cellular fatty acids were iso-C_16:0, iso-C_14:0, anteiso-C_15:0 and iso-C_15:0. Consequently, strain YC537^T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces boluensis sp. nov. is proposed. The type strain is YC537^T (= KCTC 39750 ^T = DSM 102303 ^T).

Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili

A novel actinobacterial strain, designated 13K301^T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301^T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301^T belongs to the genus Streptomyces and had highest sequence similarity to 'Streptomyces qaidamensis' S10^T (99.2 %), Streptomyces flavovariabilis NRRL B-16367^T (98.9 %) and Streptomyces phaeoluteigriseus DSM 41896^T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA-DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301^T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H₈) and MK-9(H₆). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301^T should be classified as representative of a novel species of the genus Streptomyces, for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301^T (=DSM 106873^T=KCTC 49110^T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of Streptomyces galilaeus and Streptomyces bobili belong to a single species. It is, therefore, proposed that S. galilaeus be recognised as a heterotypic synonym of S. bobili for which an emended description is given.

Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential

The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.

Jiangella anatolica sp. nov. isolated from coastal lake soil

A novel actinobacterial strain, designated GTF31^T, was isolated from a coastal soil sample of Gölcük Lake, a crater lake in southwest Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences and showed that the strain is closely related to Jiangella gansuensis DSM 44835^T (99.4%), Jiangella alba DSM 45237^T (99.3%) and Jiangella muralis DSM 45357^T (99.2%). Optimal growth was observed at 28 °C and pH 7-8. Whole cell hydrolysates were found to contain LL-DAP, glucose, mannose, rhamnose and ribose. The predominant menaquinone was identified as MK-9(H₄). The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycophospholipids and unidentified phospholipids. The major fatty acids were identified as anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0. The G + C content of the type strain was determined to be 72.5% and the size of the draft genome is 7.0 Mb. The calculated digital DDH values between strain GTF31^T and the type strains of J. gansuensis, J. alba, J. muralis and Jiangella alkaliphila ranged from 24.4 to 34.4% and ANI values ranged between 81.0 and 87.9%. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain GTF31^T (= DSM 100984^T = CECT 9378^T) is proposed to represent the type strain of a novel species, Jiangella anatolica sp. nov.