Section Review; Anti-infectives: Review of actinomycetes compounds 1990 – 1995

Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry

A total of 416 actinomycete cultures were isolated from various unique environments in Ethiopia and tested for bioactivity. Six isolates with pronounced antimicrobial activity were chosen for taxonomic identification and further investigation. Morphological and cultural properties of the isolates were found to be consistent with those of the genus Streptomyces, which was further confirmed by phylogenetic analysis based on 16S rRNA gene sequences. One of the isolates, designated Streptomyces sp. Go-475, which displayed potent activity against both pathogenic yeasts and Gram-positive bacteria, was chosen for further investigation. Metabolite profiles and bioactivity of Go-475 incubated on wheat bran-based solid and soya flour-based liquid media were compared using high-resolution LC-MS. This allowed identification of several known compounds, and suggested the ability of Go-475 to produce new secondary metabolites. Major anti-bacterial compounds were purified from liquid cultures of Go-475, and their structures elucidated by NMR and HRMS as 8-O-methyltetrangomycin and 8-O-methyltetrangulol. In addition, many potentially novel metabolites were detected, the majority of which were produced in solid media-based fermentation. The genome sequence of Streptomyces sp. Go-475 was obtained using a hybrid assembly approach of high quality Illumina short read and low quality Oxford Nanopore long read data. The complete linear chromosome of 8,570,609 bp, featuring a G+C content of 71.96%, contains 7,571 predicted coding sequences, 83 t(m)RNA genes, and six rrn operons. Analysis of the genome for secondary metabolite biosynthesis gene clusters further confirmed potential of this isolate to synthesize chemically diverse natural products, and allowed to connect certain clusters with experimentally confirmed molecules.

Streptomyces amphotericinicus sp. nov., an amphotericin-producing actinomycete isolated from the head of an ant (Camponotus japonicus Mayr)

A novel actinomycete, designated strain 1H-SSA8^T, was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce amphotericin. A polyphasic approach was employed to determine the status of strain 1H-SSA8^T. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces. The menaquinones detected were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, C15 : 0 and anteiso-C15 : 0. Analysis of the 16S rRNA gene sequence showed that strain 1H-SSA8^T belongs to the genus Streptomyces with high sequence similarity to Streptomyces ramulosus NRRL B-2714^T (99.2 %). Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with Streptomyces himastatinicus ATCC 53653^T (98.7 %). The MLSA utilizing partial sequences of the housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also supported the position. However, evolutionary distances were higher than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. Moreover, the low level of DNA-DNA relatedness and phenotypic differences allowed the novel isolate to be differentiated from its most closely related strain S. ramulosus NRRL B-2714^T and strain S. himastatinicus ATCC 53653^T. It is concluded that the organism can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces amphotericinicus sp. nov. is proposed. The type strain is 1H-SSA8^T (=CGMCC 4.7350^T=DSM 103128^T).

Isolation, screening and partial purification of antimicrobial antibiotics from soil Streptomyces sp. SCA 7

Thirty-seven actinomycetes strains were isolated from soil samples collected from an agriculture field in Vengodu, Thiruvannamalai District, Tamil Nadu, India (latitude: 12° 54' 0033″, North; longitude: 79° 78' 5216″, East; elevation: 228.6/70.0 ft/m). The isolates were assessed for antagonistic activity against five Gram-positive bacteria, seven Gram-negative bacteria, and two pathogenic fungi. During the initial screening, 43% of the strains showed weak activity, 16% showed moderate activity, 5% showed good activity, and 35% showed no antagonistic activity. Among the strains tested, SCA 7 showed strong antimicrobial activity. Maximum biological activity was obtained on modified nutrient glucose agar (MNGA) medium. The mycelia of SCA 7 were extracted with methanol and tested against microbial pathogens using the disc diffusion method. The crude extract was purified partially using column chromatography and assessed for antimicrobial activity. Fraction 10 showed good activity against Staphylococcus epidermidis (31.25 μg/mL) and Malassezia pachydermatis (500 μg/mL) and the active principle (fraction 10) was identified as 2,4-bis (1,1-dimethylethyl) phenol. Based on morphological, physiological, biochemical, cultural, and molecular characteristics (16S rDNA sequencing), this strain was identified as Streptomyces sp. SCA 7. It could be used in the development of new substances for pharmaceutical or agricultural purposes.

Taxonomy and chemical characterization of new antibiotics produced by Saccharothrix SA198 isolated from a Saharan soil

Actinomycete strain SA198, isolated from a Saharan soil sample of Algeria, exhibited antimicrobial activity against Gram-positive and Gram-negative bacteria, and phytopathogenic and toxinogenic fungi. The morphological and chemotaxonomic characteristics of the strain were consistent with those of the genus Saccharothrix. Analysis of the 16S rRNA gene sequence of strain SA198 showed a similarity level ranging between 97.2 and 98.8% within Saccharothrix species, S. australiensis being the most closely related. Two new active products were isolated by reverse HPLC using a C18 column. The ultraviolet-visible (UV-VIS), infrared (IR), mass, and (1)H and (14)C nuclear magnetic resonance (NMR) spectra showed that these products were new bioactive compounds. The minimum inhibitory concentrations of these antibiotics showed a strong activity against fungi and moderate activities against Gram-positive and Gram-negative bacteria.

Streptomyces qinglanensis sp. nov., isolated from mangrove sediment

A Streptomyces-like strain, 172205(T), was obtained from mangrove soil collected at Qinglan Harbour, Wenchang, Hainan, China. The strain was characterized by white aerial mycelium and long spore chains. Comparison of 16S rRNA gene sequences indicated that the strain represents a novel member of the genus Streptomyces, exhibiting highest levels of similarity (<98.29%) to the type strains of members of the genus Streptomyces. However, DNA-DNA relatedness and phenotypic data readily distinguished strain 172205(T) from phylogenetically related type strains. The predominant menaquinones were MK-9(H(6)) and MK-9(H(8)). The major fatty acids were iso-C(15:0) (10.31%), anteiso-C(15:0) (35.19%), iso-C(16:0) (20.24%) and anteiso-C(17:0) (10.05%). The diagnostic phospholipid was phosphatidylethanolamine. The cell wall contained ll-diaminopimelic acid and meso-diaminopimelic acid and whole-cell hydrolysates contained ribose, galactose and glucose. The results of DNA-DNA hybridization, physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 172205(T) from phylogenetically related type strains. Therefore, strain 172205(T) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces qinglanensis sp. nov. is proposed. The type strain is 172205(T) (=CGMCC 4.6825(T) =DSM 42035(T)).

Isolation and partial characterization of pigment-like antibiotics produced by a new strain of Streptosporangium isolated from an Algerian soil

AIMS

Identification of a new actinomycete strain Sg3, belonging to the genus Streptosporangium and partial characterization of the produced antibacterial activities.

METHODS AND RESULTS

The strain Sg3 was isolated from an Algerian Saharan soil and identified by morphological, chemotaxonomic and phylogenetic analyses to the genus Streptosporangium. The comparison of its physiological characteristics with those of known species of Streptosporangium showed significant differences with the nearest species Streptosporangium carneum. Analysis of the 16S rDNA sequence of strain Sg3 showed a similarity level ranging between 97% and 98.8% within Streptosporangium species, with S. carneum the most closely related. Strain Sg3 showed a red coloured antibacterial activity against gram-positive bacteria on several culture media. The purification of the red pigment by chromatographic methods led to the isolation of three active products. The (1)H nuclear magnetic resonance (NMR), mass, infrared (IR) and ultraviolet-visible (UV-VIS) data of these molecules strongly suggested that they belonged to the quinone-anthracycline group with three or more rings.

CONCLUSIONS

Strain Sg3 represents a distinct phyletic line suggesting a new genomic species. It produces antibacterial activities identified as quinone-anthracycline aromatics.

SIGNIFICANCE AND IMPACT OF THE STUDY

The quinone-anthracycline antibiotics are known for their antimicrobial and antineoplastic activities and are used in chemotherapy for the treatment of many cancer diseases. The present work constitutes the first stage of a whole series of studies to be realized on these antibiotics before arriving at a possible application.

Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade-specific PCR primers

The Streptomyces violaceusniger 16S rRNA gene clade contains organisms that are of ecological interest and a rich source of novel bioactive metabolites. Improvements in the classification of members of the S. violaceusniger clade made it possible to design, evaluate and use an oligonucleotide primer set to gain an insight into the presence, distribution and taxonomic diversity of members of this taxon in environmental samples. In silico testing showed that the primers had a perfect match with representatives of the S. violaceusniger clade. The primers, designated S-S-Svio-66-a-S-20 and S-S-Svio-1274-a-A-20, amplified an approximately 1190-bp stretch of 16S rRNA gene from authenticated members of the S. violaceusniger clade, but not from representatives of other actinomycete taxa. Following amplification of DNA extracted from sediment and soil samples, the sequences of cloned PCR products confirmed the specific amplification of target sequences in 87% of the clones; the use of 16S rRNA gene fragment similarity correlations indicated that the clones represented new species. The primers can be used to facilitate the isolation of novel members of the S. violaceusniger 16S rRNA gene clade by allowing prescreening of environmental samples and the subsequent detection and retrieval of targetted strains through the use of selective isolation procedures.

The genus Amycolatopsis: Indigenous plasmids, cloning vectors and gene transfer systems

The genus Amycolatopsis is a member of the phylogenetic group nocardioform actinomycetes. Most of the members of the genus Amycolatopsis are known to produce antibiotics. Additionally, members of this genus have been reported to metabolize aromatic compounds as the sole sources of carbon and energy. Development of genetic manipulation in Amycolatopsis has progressed slowly due to paucity of genetic tools and methods. The occurrence of indigenous plasmids in different species of Amycolatopsis is not very common. Till date, only three indigenous plasmids viz., pMEA100, pMEA300 and pA387 have been reported in Amycolatopsis species. Various vectors based on the indigenous plasmids, pMEA100, pMEA300 and pA387, have been constructed. These vectors have proved useful for molecular genetics studies of actinomycetes. Molecular genetic work with Amycolatopsis strains is not easy, since transformation methods have to be developed, or at least optimized, for each particular strain. Nonetheless, methods for efficient transformation (polyethyleneglycol (PEG) induced protoplast transformation, transformation by electroporation and direct transformation) have been developed and used successfully for the introduction of DNA into several Amycolatopsis species. The construction of plasmid cloning vectors and the development of gene transfer systems has opened up possibilities for studying the molecular genetics of these bacteria.

Antimicrobial compounds produced by Actinomadura sp. AC104 isolated from an Algerian Saharan soil

During a search for nonpolyenic antifungal antibiotics, an actinomycete designated AC104 was isolated from a Saharan soil sample by a dilution agar plating method using a chitin - vitamins B medium supplemented with rifampicin. Isolate AC104 presented the morphological and the chemical characteristics of the genus Actinomadura. On the basis of 76 physiological tests and 16S rDNA analysis, this isolate was determined to be quite different from the known species of Actinomadura. It is active against filamentous fungi and both Gram-positive and Gram-negative bacteria. The production of antibiotic substances was investigated using several culture media. The highest antimicrobial activities were obtained on ISP2 medium. The benzenic extract contained five bioactive spots detected on thin layer chromatography plates. Among these antibiotics, a complex called 104A, which showed the more interesting antifungal activity, was selected and purified by reverse-phase high-pressure liquid chromatography. This complex is composed of four compounds. Ultraviolet-visible, infrared, mass, and 1H nuclear magnetic resonance spectroscopy studies showed that these molecules contain an aromatic ring substituted by aliphatic chains. These compounds differ from the known antibiotics produced by Actinomadura species.

Actinomycetes isolated from lichens: evaluation of their diversity and detection of biosynthetic gene sequences

Actinomycetes, one of the major communities of the microbial population present in soil, can also be found inhabiting a wide diversity of ecological sources. We have explored the use of lichens as an alternative source for the isolation of novel actinomycetes. Lichens are symbiotic mixtures of fungi, green algae and/or cyanobacteria and whereas these symbiotic components have been extensively described, the microbial community inhabiting this niche has not been well characterized. We studied the diversity of the actinomycete population isolated from lichens collected in tropical areas from the Hawaii and Reunion islands and in cold areas from Alaska. The diversity of the microbial population was evaluated using fatty acid analysis and molecular fingerprinting. A PCR approach to screen the isolates for genes associated with secondary metabolite production was applied to evaluate the biosynthetic potential of these strains; profiles obtained for each isolate were compared to the antimicrobial activity exhibited by these isolates in laboratory conditions. Our results demonstrate that lichens represent an extremely rich reservoir for the isolation of a wide diversity of actinomycetes many of them representing still today a rich untapped source of secondary metabolites.

Small bugs, big business: the economic power of the microbe

The versatility of microbial biosynthesis is enormous. The most industrially important primary metabolites are the amino acids, nucleotides, vitamins, solvents, and organic acids. Millions of tons of amino acids are produced each year with a total multibillion dollar market. Many synthetic vitamin production processes are being replaced by microbial fermentations. In addition to the multiple reaction sequences of fermentations, microorganisms are extremely useful in carrying out biotransformation processes. These are becoming essential to the fine chemical industry in the production of single-isomer intermediates. Microbially produced secondary metabolites are extremely important to our health and nutrition. As a group, they have tremendous economic importance. The antibiotic market amounts to almost 30 billion dollars and includes about 160 antibiotics and derivatives such as the beta-lactam peptide antibiotics, the macrolide polyketide erythromycin, tetracyclines, aminoglycosides and others. Other important pharmaceutical products produced by microrganisms are hypocholesterolemic agents, enzyme inhibitors, immunosuppressants and antitumor compounds, some having markets of over 1 billion dollars per year. Agriculturally important secondary metabolites include coccidiostats, animal growth promotants, antihelmintics and biopesticides. The modern biotechnology industry has made a major impact in the business world, biopharmaceuticals (recombinant protein drugs, vaccines and monoclonal antibodies) having a market of 15 billion dollars. Recombinant DNA technology has also produced a revolution in agriculture and has markedly increased markets for microbial enzymes. Molecular manipulations have been added to mutational techniques as means of increasing titers and yields of microbial procresses and in discovery of new drugs. Today, microbiology is a major participant in global industry. The best is yet to come as microbes move into the environmental and energy sectors.

Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity

AIMS

To evaluate the patterns of the production of antimicrobial compounds by diverse collection of actinomycetes isolated from different geographies under alternative conditions of pH and salinity in the media.

METHODS AND RESULTS

Actinomycetes were grouped based on their method of isolation and their phenotype diversity was determined by total fatty acid analysis. A total of 335 representative isolates, including 235 Streptomyces species and 100 actinomycetes from other taxa, were screened for the production of antimicrobial activities against a panel of bacteria, filamentous fungi and yeasts, including some of clinical relevance. Production of antimicrobial activities was detected in 230 strains. In the case of the genus Streptomyces, 181 antimicrobial activities (77% of the tested isolates) were recorded. The activities observed among the other actinomycetes taxa were lower (49% of the tested isolates).

CONCLUSIONS

The results of this study support the idea that species of actinomycetes isolated in alternative selective conditions of pH and salinity present a significant capacity to produce compounds with antibacterial or antifungal activity. The best group of isolates in terms of production of active secondary metabolites was the one isolated in saline conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results demonstrate that these actinomycetes strains isolated in alternative selective conditions of pH and salinity and collected from diverse geographical locations present a significant capacity to produce compounds with antibacterial or antifungal activity.

Improved secondary metabolite production in the genus Streptosporangium by optimization of the fermentation conditions

The cultivation of strains of the genus Streptosporangium in batch fermentations demonstrated that the optimal conditions for secondary metabolite production are completely different to those of the closely related genus Streptomyces. The dissolved oxygen tension (pO(2)) was identified as an important parameter for optimal production of secondary metabolites in submerged cultures. Extreme variations of this parameter by changes in aeration (gas flow), agitation system and stirrer speed showed a tremendous impact in production yields of all investigated strains. Finally, a 20-fold increase in productivity was observed by conditions of controlled oxygen excess compared to optimal fermentation conditions for Streptomyces strains.

Screening of new bioactive materials from microbial extracts of soil microorganism (I). Antimicrobial activity from 200 samples using microdilution assay

The microdilution assay recommended by NCCLS (National Committee for Clinical Laboratory Standards) is one of the standardized methods of antibiotic susceptibility test. This method has been widely used clinically to obtain MIC values of antibiotics on pathogenic microorganisms. It is more convenient, rapid and simple to test many samples than other test methods such as agar diffusion assay and broth macrodilution assay. The screening of antimicrobial agents from microbial extracts is too laborious in its process. Therefore, a number of screening methods having more simple procedure have been developed. In our laboratory, we applied microdilution assay for screening the antimicrobial agents. This assay showed dose-response results and was more sensitive than disc diffusion assay in our system. We tested 200 samples of microbial extracts originated from 100 microbial strains and selected several samples as potential candidates. In this report, we show that the microdilution assay is more convenient method in screening of antibiotic susceptibility than those previously reported.