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Neighbour-joining phylogenetic tree based on near-complete 16S rRNA gene sequences showing the relationship between strain RB72 T and 24 species of the genus Streptomyces. Numbers at nodes indicate levels of bootstrap support (%) based on analysis of 1000 resampled datasets; only values above 50 % are given. NCBI accession numbers for each sequence are in parentheses. Bar, 1 substitution per 1000 nt.
Source publication
Actinomycete strain RB72(T) was isolated from woodland bluff soil in northern Alabama, USA, and shown to produce a broad spectrum bacteriocin. Based on morphological and chemotaxonomic characteristics, the strain was determined to belong to the genus Streptomyces. Phylogenetic analysis of the near-complete 16S rRNA gene sequence indicated that it d...
Citations
... nov. [15], Streptomyces griseus (grisemycin) [16], and Streptomyces bottropensis (bottromycin A2) [17]. These studies show that Streptomyces bacteriocins have broad spectrum antibacterial activity against Gram-positive and negative bacteria and even resistant pathogenic bacteria, such as methicillin-resistant Staphylococcus aureus [14]. ...
Bacteriocin-like inhibitory substances (BLIS) have sparked great interest because of their promising use in food as natural antimicrobial agents. In this work, six Streptomyces isolates obtained from the gut of Chanos chanos demonstrated their ability to produce extracellular metabolites with inhibitory activity against Salmonella enterica serovar Typhimurium, Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus. Exposure of the extracellular metabolites to proteolytic enzymes (i.e., proteinase-K, trypsin, and pepsin) revealed high sensitivity and confirmed their proteinaceous nature. The metabolites were stable at high temperatures (up to 100°C for 30 min) and a wide range of pH (pH 2.0–7.0). Fractionation of the crude BLIS by filtration yielded three fractions based on molecular weight: <3 kDa, 3–10 kDa, and >10 kDa. Analysis of the antibacterial activity of these fractions showed increased specific activity, especially in the fraction with a molecular weight (MW) of <3 kDa, relative to the crude sample. The fraction with MW<3 kDa had minimum inhibitory and bactericidal concentrations in ranges 0.04–0.62 mg·mL⁻¹ and 0.08–1.25 mg·mL⁻¹, respectively. This fraction also showed better temperature and pH stability compared with crude BLIS. Brine shrimp toxicity assay revealed that this fraction has moderate toxicity with a 50% lethal concentration of 226.975 μg·mL⁻¹ (i.e., moderate toxicity) to Artemia salina. Identification of the peptide sequences of this fraction by liquid chromatography–tandem mass spectrometry yielded 130 proteins with retention times of 15.21–19.57 min. Eleven proteins with MWs of 1345.66–2908.35 Da and composed of less than 30 amino acid residues with high hydrophobicity (15.34–26.22 kcal·mol⁻¹) appeared to be responsible for the antibacterial activity of the fraction. This study revealed the potential application of BLIS from Streptomyces, especially BLIS SCA-8, as antibacterial agents.
... Streptomyces spp. can be further distinguished by physiological and genetic characteristics including high DNA %G + C content (69-78%) [8], LL-diaminopimelic acid (L-DAP) in their peptidoglycan [9,10], and the amounts of saturated iso-and anteisobranched fatty acids [11]. As such, polyphasic taxonomic studies have been critical for the classification of new Streptomyces species by comparing the phenotypic and genotypic characteristics of a presumably novel isolate to closely related type strains of previously described species [10,12]. ...
Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794T, Streptomyces laculatispora NRRL B-24909T, and Streptomyces brevispora NRRL B-24910T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04T (= DSM 111306T = CCM 9048T) as the type strain.
... Three different production media, i.e., nutrient broth with glucose (Farris et al. 2011), YEME broth (Shirling and Gottlieb, 1966), and gause's synthetic broth (Dholakiya et al. 2017) were used to determine the optimum production media. Each isolate was inoculated on the medium and incubated for 10 days at 30°C. ...
Streptomyces has been recognized as a promising and productive source of antibacterial and antioxidant compounds. The phenotypic and genomic characterizations indicated AIA12 and AIA17 are closely related to the S. globisporus ARGB01 and S. misionensis S1-SC15, respectively. Incubation on yeast-malt extract broth for nine days (AIA12) and 11 days (AIA17) proved to be the best growth medium and optimum antibacterial production time for these two strains. Crude-extract of extracellular secondary metabolites, obtained by ethyl acetate extraction, demonstrated broad-spectrum inhibitory activity against Pseudomonas aeruginosa InaCC B52, Staphylococcus aureus ATCC 25923, Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, Salmonella Typhimurium ATCC 14028, and Listeria monocytogenes with minimum inhibitory and minimum bactericidal concentrations from 2.5 to 0.31 and 5.0 to 0.31 mg mL-1 , respectively. Evaluation of antioxidant showed AIA17 crude-extract had moderate DPPH scavenging and antioxidant activities of 65.122% ± 0.56 and 28.178 ± 0.24 mg ascorbic acid equivalent antioxidant capacity (AEAC g-1), respectively. The identification of compounds through profiling with RP-HPLC showed optimum absorbance at 210 and 214 nm, which showed the presence of peptide groups in the constituent compounds' molecular structure. These findings indicate that Chanos chanos-derived Streptomyces produces valuable bioactive compounds with various promising biological activities.
... Some RiPPs which are produced by Streptomyces have been reported, such as siamycin-I by Streptomyces sp. [18], cinnamycin by S. cinnamoneus [19], bottromycin by S. bottropensis [20], bacteriocin-like by S. scopuliridis [21], grisemycin by S. griseus [22], telomestatin by S. anulatus [23], and archromosin by S. achromogenes [24]. ...
Streptomyces has been reported as an essential producer of bioactive substances, including antibiotics and other types of antimicrobials. This study investigated antibacterial-producing Streptomyces isolated from the gut of estuarine fish Chanos chanos, emphasizing screening for the producer of peptide-containing antibacterial compounds. Eighteen isolates were found during preliminary screening, in which four isolates showed the best antibacterial activities. Based on the morphological, physiological, and biochemical characterization, as well as 16S rRNA partial sequencing, all of the four isolates belonged to Streptomyces. Three isolates were suspected as novel isolate candidates based on homology presentations and phylogenetic tree analysis. Disk-diffusion assay of the metabolite-crude-extract from the isolates showed broad-spectrum inhibitory activities against Staphylococcus aureus ATCC 25923, Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa InaCC B52 with minimum inhibitory concentration and minimum bactericidal concentration ranging from 2.5-10 mg/mL and 5-10 mg/mL, respectively. The highest antibacterial activity with low MIC and MBC values was shown by isolate AIA-10. Qualitative HPLC profiling revealed that the metabolic-crude-extracts showed many peaks with intensive area at 210 and 214 nm, especially from SCA-11 and AIA-10, indicating the presence of peptide groups in the structure of the constituent compound. The results also suggested that crude extracts SCA-11 and AIA-10 had higher hydrophobicity properties than the other extracts. Further characterization of the active compound was needed to find out which compounds were responsible for the antibacterial activity. The results of this study indicated that some Streptomyces isolated from new environmental niches, i.e., gut of estuarine fish Chanos chanos, produce promising peptide-containing bioactive compounds.
... In the case of streptomycetes, their practical application as probiotics in aquaculture was scarcely studied despite their potential to produce a variety of bioactive compounds. Not only antibiotics, but streptomycetes also represent the antibacterial activity via siderophore production (Yang et al., 2019) and the bacteriocin production (Farris et al., 2011). In a previous research, Das et al. (2010) conveyed the beneficial effects of streptomycetes-supplemented feed on black tiger shrimp, Penaeus monodon, with improved length, wet weight, and survival rate with/without the challenge of Vibrio harveyi. ...
This study scoped the isolation of aerobic actinomycetes with probiotic properties against bacterial pathogens in Nile tilapia. Eleven rhizosphere soil samples were collected from the agricultural sites in three provinces (Chanthaburi, Nan, and Chachoengsao) of Thailand. A total of 157 actinomycete-like colonies were successfully isolated. The antibacterial testing against four tested bacteria (Streptococcus agalactiae 2809, Aeromonas jandaei 1929, Aeromonas veronii 1930, and Edwardsiella ictaluri 2234) was carried out by a modified cross-streaked method. The results showed that 108 strains possessed antibacterial activity against at least one of the bacterial pathogens. Seventeen active isolates were identified in the actinomycetes by the analysis of the partial 16S ribosomal rRNA gene, and the phylogenetic relationships of the isolates and their closely related strains were confirmed by the neighbor-joining method. Isolates LNW002 and YNW004 survived in the liquid cultivation with International Streptomyces Project 2 at pH 2 and the presence of 0.3% bile salt for 2 hours, which mimics the gastric acidity and bile salt in the gastrointestinal tract of Nile tilapia in vitro. In conclusion, these strains might be further investigated for their efficacy as probiotics in Nile tilapia. This study is the first to report on anti-E. ictaluri activity in streptomycetes.
... In spite of the importance and versatility of these compounds, few bacteriocins produced by the genus Streptomyces have been identified and characterized (Onaka et al. 2005;Claesen and Bibb 2011;Soohyun et al. 2013;Farris et al. 2011), and little is known about their structural characteristics, antimicrobial Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12223-020-00770-z) contains supplementary material, which is available to authorized users. ...
Streptomyces spp. are Gram-positive bacteria well-known for their ability to produce antibiotics and other metabolites, but few studies on bacteriocins produced by these bacteria have been reported. We tested eight Streptomyces strains against different pathogenic bacteria, and selected S. griseus, S. nigrescens, S. bottroprensis, and S. violaceoruber for further study based on their inhibitory effects against bacteria, including human pathogens. S. bottropensis reached its highest activity at 312 h and was higher than the activities of S. violaceoruber and S. nigrescens. The best condition for bacteriocin precipitation was using diammonium sulfate at 50% saturation. Bacteriocins were susceptible to proteinase treatments and stable at high temperature (up to 100 °C). The highest inhibitory activities were observed between pH 5 and 6. Cross-activity assays indicated that each Streptomyces strain produced different bacteriocins. When preparations of S. griseus and S. nigrescens were subjected to SDS-PAGE, bands of inhibition were observed in the gel overlay assay at a position corresponding to ~ 2 and 3 kDa, respectively, suggesting that both strains are potential sources for novel bacteriocins.
... Tolerance of sodium chloride was established using basal medium 5339 (casein peptone 10 g/L, yeast extract 5 g/L, agar 15 g/L) supplemented with 0-15% (w/v) sodium chloride in 2.5% intervals. The physiological parameter of pH was tested in tubes with ISP2 medium (Shirling and Gottlieb 1966) at pH levels from 4 to 12. Phenotypic characteristics of Streptomyces spheroides (NRRL-2449 T ), Streptomyces scopuliridis (NRRL B-24574 T ), Streptomyces odonnellii (NRRL B-24891 T ) and Streptomyces niveus (NRRL-2466 T ) were re-assessed and compared with the original descriptions (Farris et al. 2011;Harris et al. 1955;Pereira et al. 2017;Smith 1956). ...
... The physiological properties of these strains are summarised in Tables 2 and 3. One notable observation was the S. scopuliridis NRRL B-24574 T displayed differences in fructose, mannitol and arabinose relative to the original description (Farris et al. 2011) ( Table 2). The source of these differences is not clear, but the genome of S. scopuliridis NRRL B-24574 T (JOEI01) shows a fructose utilisation pathway with PTS transporter and the genes to utilise mannitol (data not shown). ...
... No significant phenotype differences were ? good growth and positive utilisation, È poor to fair growth, É faint growth and probably no utilisation, -no growth a Farris et al. (2011) observed among isolates AC161, AC162, AC208 and AC230 T (data not shown). Sequencing the genomic DNA of AC230 T yielded a draft genome consisting of 480 scaffolds and a size of 7.74 Mbp. ...
Four bacterial strains, with the capability of inhibiting Pseudogymnoascus destructans, the causative agent of white-nose syndrome, were isolated from male Townsend’s big-eared bats (Corynorhinus townsendii, Family: Vespertilionidae) in New Mexico. Isolates AC161, AC162, AC208, and AC230T were characterised as a novel clade using morphological, phenotypic and phylogenetic analysis. A draft genome of the type strain was completed to determine its taxonomy and secondary metabolite biosynthetic potential. Multi-locus sequence analysis nests AC230T with neighbours Streptomyces scopuliridis (NRRL B-24574T), Streptomyces lushanensis (NRRL B-24994T), Streptomyces odonnellii (NRRL B-24891T) and Streptomyces niveus (NRRL 2466T). Further phylogenetic analysis showed the MLSA distances between AC230T and its near neighbours are much greater than the generally accepted threshold (> 0.007) for bacterial species delineation. DNA–DNA relatedness between AC230T and its near neighbours ranged between 25.7 ± 2.1 and 29.9 ± 2.4%. The DNA G+C content of the genomic DNA of the type strain is 71.7 mol%. Isolate AC230T presents a white to ivory hue on most ISP media and its micromorphology exhibits ovoid spores with smooth surfaces in flexuous chains. Based on our study of AC230T, the strain warrants the assignment to a novel species, for which the name Streptomyces corynorhini sp. nov. is proposed. The type strain is AC230T (= JCM 33171T, = ATCC TSD155T).
... For example, an informatipeptin pathway has been predicted in S. kebangsaanensis based on S. gancidicus BKS 13-15 and S. prunicolor NBRC 13075 gene clusters ( Fig. 3). Bacteriocin has been isolated from most bacteria and archaea, each of which exhibited different structure, size, and mode of action as well as mechanism ( Farris et al., 2011;Nes, Yoon & Diep, 2007). The presence of bacteriocin genes in S. kebangsaanensis in different scaffolds thus suggests the potential for this strain to produce different types of bacteriocin. ...
Background
Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis , an endophyte isolated from the ethnomedicinal Portulaca oleracea.
Methods
The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites.
Results
The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis.
Discussion
The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
... Overall, many of the isolates were closely related or identical to known strains (not obtained from lichens) producing Table 3 Composition of actinomycetes isolated from three lichen genera including 11 lichen samples collected in different localities Lichen genus Samples Sampling localities Genus [55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71] have been described from the closely related species among the 40 potential novel Actinobacteria strains (Table 4). Significantly, a number of gene clusters in natural product biosynthesis, including polyketide synthases of type I, type II, and non-ribosomal peptide synthetases are present, and the biosynthetic genes of natural products are much more common among the novel actinomycete strains (72.5%) than the average detective rate (60.1%), which will further the evidence of their biosynthetic potential. ...
Lichens are structured associations of a fungus with a cyanobacteria and/or green algae in a symbiotic relationship, which provide specific habitats for diverse bacterial communities, including actinomycetes. However, few studies have been performed on the phylogenetic relationships and biosynthetic potential of actinomycetes across lichen species. In the present study, a total of 213 actinomycetes strains were isolated from 35 lichen samples (22 lichen genera) collected in Yunnan Province, China. 16S rRNA gene sequence analysis revealed an unexpected level of diversity among these isolates, which were distributed into 38 genera, 19 families, and 9 orders within the Actinobacteria phylum. The detailed taxa of isolates had no clear relationship to the taxonomic affiliations of the associated lichens. To the best of our knowledge, this is the first report to describe the isolation of Actinophytocola, Angustibacter, Herbiconiux, Kibdelosporangium, Kineosporia, Kitasatospora, Nakamurella, Nonomuraea, Labedella, Lechevalieria, Lentzea, Schumannella, and Umezawaea species from lichens. At least 40 isolates (18.78%) are likely to represent novel actinomycetes taxa within 15 genera. In addition, all 213 isolates were tested for antimicrobial activity and screened for genes associated with secondary metabolite production to evaluate their biosynthetic potential. These results demonstrate that the lichens of Yunnan Province represent an extremely rich reservoir for the isolation of a significant diversity of actinomycetes, including novel species, which are potential source for discovering biologically active compounds.
... Streptomyces sp. strain 212 was isolated from Rainbow Bluff, a woodland rock outcropping in Lynn, Alabama, using the methods described by Farris et al. (2011). The strain was maintained on nutrient agar plates and cultivated in nutrient broth with 5% dextrose for genomic DNA isolations used in de novo genome sequencing assays. ...
Unlabelled:
An open reading frame with homology to known endolysin genes was identified in the genome of Streptomyces sp. strain 212, which is a newly isolated soil bacterium. The heterologously expressed gene product of this endolysin-like gene, called Mitrecin A, demonstrated bacteriolytic activity against several Gram-negative bacteria. The genome of the bacterial strain was sequenced to draft quality using pyrosequencing followed by genome assembly and gene annotation. Within the sequence, a chromosomally located endolysin-like open reading frame was predicted. The gene product, designated Mitrecin A, was heterologously expressed and isolated from contaminating proteins as a fusion protein to a 6-histidine tag. Mitrecin A consists of 127 amino acids arranged in modular domains of activity. It has an estimated molecular weight of 14.3 kDa and retains sequence homology to the M15C peptidase subfamily of zinc metallocarboxypeptidases. The heat-labile purified recombinant protein has an overall positive charge, has optimal catalytic activities at 26°C in solution of pH 9 with 1% saline and has bacteriolytic activity against Gram-negative bacteria of the medically important genera Aeromonas, Escherichia, Salmonella, Shigella, Vibrio and Yersinia.
Significance and impact of the study:
The gene of a new protein antimicrobial, Mitrecin A, was discovered in the genome of a soil bacterium. The purified recombinant enzyme, resulting from heterologous over expression of the gene, was found to be tolerant of increased pH conditions and to have bacteriolytic activity against Gram-negative bacteria of the medically important genera Aeromonas, Escherichia, Salmonella, Shigella, Vibrio and Yersinia. Characterization of enzymes such as Mitrecin A from previously uncharacterized bacteria provides potential options for new biocontrol agents in medically and economically important applications like therapeutics, disinfectants, food preservatives, agricultural livestock antimicrobials, and inhibitors of biofilm production.
