Streptomyces tunisialbus sp. nov., a novel Streptomyces species with antimicrobial activity

The intricate molecular identification of Streptomyces: a case study on Antarctic soil isolates

Despite the worldwide use of 16S rRNA to identify bacterial species, the use of this gene does not discriminate the 750 species in the genus Streptomyces. A MLST scheme was constructed with rpoB, gyrB, recA, trpB and atpD genes to access the genomic variances in Streptomyces species evolution. We analyze the housekeeping genes in 49 Streptomyces isolates from Antarctic soil. It was used two different databases, GenBank and EzBioCloud to compare the 16S sequences. The species founded in both databases are not the same, but in both cases, a few isolates achieve the necessary high percentage to consider the identification. There is a lack of deposited sequences in the other genes, as the data in GenBank proved to be insufficient. Isolate LMA323St_9 has the potential to be studied as a novel species. Besides that, the use of housekeeping genes gives robust phylogenetic information to understand in group relationships.

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 barringtoniae sp. nov., isolated from rhizosphere of plant with antioxidative potential

A novel actinomycete strain, JA03T, belonging to the genus Streptomyces , was isolated from the rhizosphere of Barringtonia racemosa (L.) Spreng. It was characterized taxonomically using a polyphasic approach. It grew at 25–37 °C, at pH 5–10 and with 6 % (w/v) NaCl. It contained ll-diaminopimelic acid in the cell-wall peptidoglycan. Ribose and glucose were detected in its whole-cell hydrolysate. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C15 : 0. Detected polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, unidentified phospholipids and unidentified amino lipids. Based on the results of 16S rRNA gene sequence analyses, strain JA03T showed highest similarity to Streptomyces filipinensis NBRC 12860T (98.76 %), Streptomyces fodineus TW1S1T (98.69 %) and Streptomyces shenzhennensis 172115T (98.68 %). Strain JA03T has a genome size of 9 092 851 bp with DNA G+C content of 71.28 mol%. The average nucleotide identity (ANI)-blast and ANI-MUMmer values of strain JA03T and related type strains were 79.6–89.2 and 86.7–92.5 %, respectively, and the digital DNA–DNA hybridization values were 27.3–46.4 %. Ethyl acetate extract of JA03T exhibited total phenolic content (33.4±0.6 µg mg−1 gallic acid equivalent), ferric reducing power value (70.8±1.8 µg mg−1 ascorbic acid equivalent) and 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity (IC50=67.0±21.1 µg ml−1). Intracellular reactive oxygen species and NO production in RAW264.7 macrophage cells induced by H2O2 and lipopolysaccharide were inhibited with IC50 of 67.40 and 16.95 µg ml−1, respectively. Based on the taxonomic results, it has been concluded that strain JA03T represents a novel species of the genus Streptomyces for which the name Streptomyces barringtoniae sp. nov., is proposed. The type strain is JA03T (=LMG 32415T=TISTR 2999T).

Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01 T , was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01 T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724 T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970 T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269 T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01 T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01 T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01 T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01 T = CCM 9049 T = DSM 111582 T ) is proposed.

Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune

A polyphasic study was designed to determine the taxonomic provenance of a strain, isolate PRKS01-29T, recovered from an Indonesian sand dune and provisionally assigned to the Streptomyces violaceusniger clade. Genomic, genotypic and phenotypic data confirmed this classification. The isolate formed an extensively branched substrate mycelium which carried aerial hyphae that differentiated into spiral chains of rugose ornamented spores, contained LL-as the wall diaminopimelic acid, MK-9 (H6, H8) as predominant isoprenologues, phosphatidylethanolamine as the diagnostic phospholipid and major proportions of saturated, iso- and anteiso- fatty acids. Whole-genome sequences generated for the isolate and Streptomyces albiflaviniger DSM 41598T and Streptomyces javensis DSM 41764T were compared with phylogenetically closely related strains, the isolate formed a branch within the S. violaceusniger clade in the resultant phylogenomic tree. Whole-genome sequences data showed that isolate PRKS01-29T was most closely related to the S. albiflaviniger strain but was distinguished from the latter and from other members of the clade using combinations of phenotypic properties and average nucleotide identity and digital DNA:DNA hybridization scores. Consequently, it is proposed that isolate PRKS01-29T (= CCMM B1303T = ICEBB-02T = NCIMB 15210T) should be classified in the genus Streptomyces as Streptomyces sabulosicollis sp. nov. It is also clear that streptomycetes which produce spiral chains of rugose ornamented spores form a well-defined monophyletic clade in the Streptomyces phylogenomic tree., the taxonomic status of which requires further study. The genome of the type strain of S. sabulosicollis contains biosynthetic gene clusters predicted to produce new natural products.

Streptomyces bathyalis sp. nov., an actinobacterium isolated from the sponge in a deep sea

A novel actinobacterium, designated ASO4wet^T, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wet^T is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413^T (98.87 %), Streptomyces glycovorans YIM M 10366^T (98.38 %), and Streptomyces abyssalis YIM M 10400^T (97.53 %). Strain ASO4wet^T contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C_16:0, anteiso-C_15:0, and iso-C_15:0. Polyphasic taxonomy was carried out between strain ASO4wet^T and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wet^T could be distinguished from currently known Streptomyces species. Strain ASO4wet^T clearly represents a novel species in genus Streptomyces. We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wet^T (= DSM 106605^T = NCCB 100657^T). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.

BiG-FAM: the biosynthetic gene cluster families database

Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonomic diversity and provides insights into the novelty of putative BGCs, through dereplication with BGCs of known function. While multiple databases exist for exploring BGCs from publicly available data, no public resources exist that focus on GCF relationships. Here, we present BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results. BiG-FAM can be accessed online at https://bigfam.bioinformatics.nl.

Streptomyces lasalocidi sp. nov. (formerly 'Streptomyces lasaliensis'), an actinomycete isolated from soil which produces the polyether antibiotic lasalocid

Strain ATCC 31180^T was isolated from soil collected in Hyde Park, Massachusetts (USA), and found to produce the polyether antibiotic lasalocid. The name 'Streptomyces lasaliensis' has been in common use since 1974, without a recognized taxonomic description. The most closely related type cultures determined by rRNA gene sequence similarity were Streptomyces longwoodensis DSM 41677^T (100 %) and Streptomyces galbus DSM 40089^T (100 %). OrthoANI values with S. longwoodensis and S. galbus were 95.50 and 94.41 %, respectively. Chemotaxonomic characteristics supported inclusion within the genus Streptomyces. The cell wall peptidoglycan contained ll-diaminopimelic acid, and the major whole-cell sugars were glucose and ribose. Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, one unidentified lipid and one unidentified glycolipid. The major menaquinones detected were MK9(H₄), MK9(H₆) and MK9(H₈). The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0, iso-C_16 : 0, iso-C_15 : 0 and anteiso-C_17 : 1. Its DNA had a G+C content of 72.6 %. Differentiation of ATCC 31180^T from the closely related species was evident from digital DNA-DNA hybridization values of 61.80 and 56.90 % for S. longwoodensis and S. galbus respectively. Significant differences were seen in the polyphasic phenotypic analyses. ATCC 31180^T produced lasalocid, grew from 10 to 45 °C, pH4-8 and in the presence of 0-10 % NaCl, 0.01 % NaN₃ and 1 % phenol. Melanin was produced; H₂S and indole were not. Nitrate was not reduced. Spore chains were retinaculum-apertum and spore surfaces were smooth. Spore colour, mycelia colour and soluble pigment production were medium-dependent. The proposed name is Streptomyces lasalocidi sp. nov.; the type strain being ATCC 31180^T (=NRRL 3382^T=DSM 46487^T).

Draft genome sequence of Streptomyces tunisialbus DSM 105760T

Streptomyces strains are well known as promising source of bioactive secondary metabolites, important in ecology, biotechnology and medicine. In this study, we present the draft genome of the new type strain Streptomyces tunisialbus DSM 105760^T (= JCM 32165^T), a rhizospheric bacterium with antimicrobial activity. The genome is 6,880,753 bp in size (average GC content, 71.85%) and encodes 5802 protein-coding genes. Preliminary analysis with antiSMASH 5.1.2. reveals 34 predicted gene clusters for the synthesis of potential secondary metabolites, which was compared with those of Streptomyces varsoviensis NRRL ISP-5346.

Taxonomic Characterization and Secondary Metabolite Analysis of NEAU-wh3-1: An Embleya Strain with Antitumor and Antibacterial Activity

Cancer is a serious threat to human health. With the increasing resistance to known drugs, it is still urgent to find new drugs or pro-drugs with anti-tumor effects. Natural products produced by microorganisms have played an important role in the history of drug discovery, particularly in the anticancer and anti-infective areas. The plant rhizosphere ecosystem is a rich resource for the discovery of actinomycetes with potential applications in pharmaceutical science, especially Streptomyces. We screened Streptomyces-like strains from the rhizosphere soil of wheat (Triticum aestivum L.) in Hebei province, China, and thirty-nine strains were obtained. Among them, the extracts of 14 isolates inhibited the growth of colon tumor cell line HCT-116. Strain NEAU-wh-3-1 exhibited better inhibitory activity, and its active ingredients were further studied. Then, 16S rRNA gene sequence similarity studies showed that strain NEAU-wh3-1 with high sequence similarities to Embleya scabrispora DSM 41855T (99.65%), Embleya hyalina MB891-A1T (99.45%), and Streptomyces lasii 5H-CA11T (98.62%). Moreover, multilocus sequence analysis based on the five other house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) and polyphasic taxonomic approach comprising chemotaxonomic, phylogenetic, morphological, and physiological characterization indicated that the isolate should be assigned to the genus Embleya and was different from its closely related strains, therefore, it is proposed that strain NEAU-wh3-1 may be classified as representatives of a novel species of the genus Embleya. Furthermore, active substances in the fermentation broth of strain NEAU-wh-3-1 were isolated by bioassay-guided analysis and identified by nuclear magnetic resonance (NMR) and mass spectrometry (MS) analyses. Consequently, one new Zincophorin analogue together with seven known compounds was detected. The new compound showed highest antitumor activity against three human cell lines with the 50% inhibition (IC50) values of 8.8-11.6 μg/mL and good antibacterial activity against four pathogenic bacteria, the other known compounds also exhibit certain biological activity.