Streptomyces tyrosinilyticus sp. nov., a novel actinomycete isolated from river sediment

Streptomyces citrinus sp. nov., with yellow diffusible pigment

An actinomycete, designated strain Q6T, was isolated from tea plant rhizosphere soil sample in Hefei, China. Strain Q6T produced straight chains of smooth-surfaced spores and grew well on International Streptomyces Project 1-7 media. Phenotypic and genotypic analyses indicated that strain Q6T represented a member of the genus Streptomyces. The 16S rRNA gene sequence data of strain Q6T indicated that strain Q6T had the highest sequence similarity to Streptomyces xanthii CRXT-Y-14T (98.9%), Streptomyces davaonensis JCM 4913T (98.9%) and Streptomyces atriruber NRRL B-24165T (98.9%), followed by Streptomyces adustus WH-9T (98.8%), Streptomyces avermitilis MA-4680T (98.6%) and Streptomyces kunmingensis NBRC 14463T (98.6%). The phylogenomic tree, using the genome blast distance phylogeny method, showed that strain Q6T represents a new branch among the Streptomyces and has the closest genetic relationship with S. kunmingensis 80-3024T. The diagnostic diamino acid was ll-diaminopimelic acid. The major menaquinones were MK-9 (H6), MK-9 (H8) and MK-8 (H6). The dominant fatty acids were C16 : 0 (18.6%), iso-C16 : 0 (18.3%), anteiso-C15 : 0 (15.4%) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 13.8%). The main polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine (PE) and phosphatidylinositol mannoside. The DNA G+C content of strain Q6T was 71.3 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequence of strain Q6T and its closely related type strains were 77.0-87.5% and 22.4-29.7%, respectively. On the basis of these data, strain Q6T represents a novel species within the genus Streptomyces, for which the name Streptomyces citrinus sp. nov. is proposed. The type strain is strain Q6T (=CGMCC 4.7886T=NBRC 116061T).

Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

The family Streptomycetaceae is a large and diverse family within the phylum Actinomycetota . The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family Streptomycetaceae were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus Streptacidiphilus and four separated from the genus Streptomyces . Compared with members of the genera Streptacidiphilus and Streptomyces , average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov.

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 boncukensis sp. nov., isolated from saltern soil

A novel Gram-stain positive, aerobic, non-motile Actinobacterium, designated strain SB3404^T, was isolated from saltern soil collected from Boncuk Saltern, Sungurlu-Çorum, Turkey, and subjected to a polyphasic taxonomic approach. The organism has shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis of strain SB3404^T showed that it is closely related to Streptomyces albus NBRC 13014^T (97.2% sequence similarity), Streptomyces xishensis YIM M 10378^T (96.7%) and Streptomyces abyssalis YIM M 10400^T (96.5%). The cell wall of the strain contained LL-diaminopimelic acid and the cell-wall sugars were glucose, mannose and ribose. The predominant menaquinones were identified as MK-9(H₈) and MK-9(H₆). The major cellular fatty acids were found to be iso-C_16:0, anteiso-C_17:0 and anteiso-C_15:0. Consequently, strain SB3404^T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces boncukensis sp. nov. is proposed. The type strain is SB3404^T (= KCTC 49371^T = JCM 34018^T).

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 lutosisoli sp. nov., a novel actinomycete isolated from muddy soil

A novel Gram-stain positive, spore-forming, aerobic actinomycete, designated strain NEAU-QTH3-11^T, was isolated from muddy soil collected from a stream in Qitaihe, Heilongjiang Province, northeast China and characterised using a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain NEAU-QTH3-11^T belongs to the genus Streptomyces and is closely related to Streptomyces rhizosphaerihabitans NBRC 109807^T (99.38%) and Streptomyces mirabilis JCM 4791^T (99.03%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain formed a cluster with S. rhizosphaerihabitans NBRC 109807^T and Streptomyces siamensis NBRC 108799^T (98.62%). The menaquinones were identified as MK-9(H₈), MK-9(H₆) and MK-9(H₄). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C_15:0, iso-C_16:0, C_16:0 and C_15:0. However, multilocus sequence analysis based on five house-keeping genes (atpD, gyrB, rpoB, recA and trpB), low DNA-DNA hybridization results and some phenotypic, physiological and biochemical properties could differentiate the strain from its close relatives in the genus Streptomyces. Therefore, strain NEAU-QTH3-11^T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lutosisoli sp. nov. is proposed, with NEAU-QTH3-11^T (=DSM 42165^T=CGMCC 4.7198^T) as the type strain.

Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds

BACKGROUND

Actinobacteria from freshwater habitats have been explored less than from other habitats in the search for compounds of pharmaceutical value. This study highlighted the abundance of actinobacteria from freshwater sediments of two rivers and one lake, and the isolates were studied for their ability to produce antimicrobial bioactive compounds.

RESULTS

16S rRNA gene sequencing led to the identification of 84 actinobacterial isolates separated into a common genus (Streptomyces) and eight rare genera (Nocardiopsis, Saccharopolyspora, Rhodococcus, Prauserella, Amycolatopsis, Promicromonospora, Kocuria and Micrococcus). All strains that showed significant inhibition potentials were found against Gram-positive, Gram-negative and yeast pathogens. Further, three biosynthetic genes, polyketide synthases type II (PKS II), nonribosomal peptide synthetases (NRPS) and aminodeoxyisochorismate synthase (phzE), were detected in 38, 71 and 29% of the strains, respectively. Six isolates based on their antimicrobial potentials were selected for the detection and quantification of standard antibiotics using ultra performance liquid chromatography (UPLC-ESI-MS/MS) and volatile organic compounds (VOCs) using gas chromatography mass spectrometry (GC/MS). Four antibiotics (fluconazole, trimethoprim, ketoconazole and rifampicin) and 35 VOCs were quantified and determined from the methanolic crude extract of six selected Streptomyces strains.

CONCLUSION

Infectious diseases still remain one of the leading causes of death globally and bacterial infections caused millions of deaths annually. Culturable actinobacteria associated with freshwater lake and river sediments has the prospects for the production of bioactive secondary metabolites.

Precursor-directed combinatorial biosynthesis of cephalosporin analogue by endolithic actinobacterium Streptomyces sp. AL51 by utilizing thiophene derivative

Natural products or their derivatives provide a reliable resource for new drugs. The multi-step chemical reaction to produce new drug is not only expensive but also release pollutants. The precursor-based combinatorial biosynthesis (PCB) is, however, a better option to produce novel natural products with potential pharmaceutical applications. The present work is an attempt to synthesize an antibacterial compound by transforming thiophene precursor using endolithic Streptomyces sp. AL51. The Streptomyces sp. AL51 was isolated from a granite rock sample collected from Mylliem, Meghalaya, India. The isolate was identified as Streptomyces sp. based on its cultural, morphological, biochemical and molecular characteristics. The bioactive compound CAx1 was extracted from the fermentation broth. The compound was characterized by bioactivity-guided fractionation and identified by infrared, UV-visible, nuclear magnetic resonance and mass spectrometry data and identified as 7-[1-(thiophene-5-yl)-1-formamido]-3-propylenyl-3-cephem-4-carboxylic acid with molecular formula C₁₅H₁₄N₂O₄S₂. The purified compound showed considerable in vitro antibacterial activity against both Gram-positive and Gram-negative bacteria showing its broad spectrum property. The obtained results provide promising baseline information for the potential use of endolithic actinobacterium for semisynthetic drug discovery. This is the first report on PCB of broad range antibacterial compound by endolithic Streptomyces strain.