Antimicrobial compounds from endophytic Streptomyces sp. BCC72023 isolated from rice ( Oryza sativa L.)

Antimicrobials from endophytes as novel therapeutics to counter drug-resistant pathogens

The rapid increase in antimicrobial resistance (AMR) projects a "global emergency" and necessitates a need to discover alternative resources for combating drug-resistant pathogens or "superbugs." One of the key themes in "One Health Concept" is based on the fact that the interconnected network of humans, the environment, and animal habitats majorly contribute to the rapid selection and spread of AMR. Moreover, the injudicious and overuse of antibiotics in healthcare, the environment, and associated disciplines, further aggravates the concern. The prevalence and persistence of AMR contribute to the global economic burden and are constantly witnessing an upsurge due to fewer therapeutic options, rising mortality statistics, and expensive healthcare. The present decade has witnessed the extensive exploration and utilization of bio-based resources in harnessing antibiotics of potential efficacies. The discovery and characterization of diverse chemical entities from endophytes as potent antimicrobials define an important yet less-explored area in natural product-mediated drug discovery. Endophytes-produced antimicrobials show potent efficacies in targeting microbial pathogens and synthetic biology (SB) mediated engineering of endophytes for yield enhancement, forms a prospective area of research. In keeping with the urgent requirements for new/novel antibiotics and growing concerns about pathogenic microbes and AMR, this paper comprehensively reviews emerging trends, prospects, and challenges of antimicrobials from endophytes and their effective production via SB. This literature review would serve as the platform for further exploration of novel bioactive entities from biological organisms as "novel therapeutics" to address AMR.

Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2

Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.

Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40

Streptomyces are factories of antimicrobial secondary metabolites. We isolated a Streptomyces species associated with the Pelargonium graveolens rhizosphere. Its total metabolic extract exhibited potent antibacterial and antifungal properties against all the tested pathogenic microbes. Whole genome sequencing and genome analyses were performed to take a look at its main characteristics and to reconstruct the metabolic pathways that can be associated with biotechnologically useful traits. AntiSMASH was used to identify the secondary metabolite gene clusters. In addition, we searched for known genes associated with plant growth-promoting characteristics. Finally, a comparative and pan-genome analysis with three closely related genomes was conducted. It was identified as Streptomyces vinaceusdrappus strain AC-40. Genome mining indicated the presence of several secondary metabolite gene clusters. Some of them are identical or homologs to gene clusters of known metabolites with antimicrobial, antioxidant, and other bioactivities. It also showed the presence of several genes related to plant growth promotion traits. The comparative genome analysis indicated that at least five of these gene clusters are highly conserved through rochei group genomes. The genotypic and phenotypic characteristics of S. vinaceusdrappus strain AC-40 indicate that it is a promising source of beneficial secondary metabolites with pharmaceutical and biotechnological applications.

Efophylins A and B, Two C2-Asymmetric Macrodiolide Immunosuppressants from Streptomyces malaysiensis

Genomics-inspired isolation led to the identification of two new natural congeneric C2-asymmetric macrodiolide immunosuppressants, named efophylins A (1) and B (2), from Streptomyces malaysiensis DSM 4137. Their structures were elucidated by spectroscopic and computational methods and were in agreement with biosynthetic predictions from the efophylin gene cluster. Compound 2 exhibited potent immunosuppressive activity and demonstrated to inhibit the activation of the NFAT and block NFAT dephosphorylation in vitro. The immunosuppressive activity of compound 2 is possibly at least in part via the CaN/NFAT signaling pathway.

An Overview of Antimicrobial Compounds from African Edible Insects and Their Associated Microbiota

The need for easily biodegradable and less toxic chemicals in drug development and pest control continues to fuel the exploration and discovery of new natural molecules. Like certain plants, some insects can also respond rapidly to microbial infections by producing a plethora of immune-induced molecules that include antibacterial and antifungal peptides/polypeptides (AMPs), among other structurally diverse small molecules. The recent recognition that new natural product-derived scaffolds are urgently needed to tackle life-threatening pathogenic infections has been prompted by the health threats posed by multidrug resistance. Although many researchers have concentrated on the discovery of AMPs, surprisingly, edible insect-produced AMPs/small molecules have received little attention. This review will discuss the recent advances in the identification and bioactivity analysis of insect AMPs, with a focus on small molecules associated with the microbiota of selected African edible insects. These molecules could be used as templates for developing next-generation drugs to combat multidrug-resistant pathogens.

Antimicrobial Potential of Streptomyces ansochromogenes (PB3) Isolated From a Plant Native to the Amazon Against Pseudomonas aeruginosa

The objective of this study was to evaluate the antibacterial action of filamentous bacteria isolated from the Byrsonima crassifolia leaf. An endophytic bacterium has been identified by classical and molecular techniques as Streptomyces ansochromogene. Screening for antibacterial action against pathogens with medical relevance (Klebsiella pneumoniae ATCC 700603, Pseudomonas aeruginosa ATCC 15692, Staphylococcus aureus ATCC 6538, Corynebacterium diphtheriae ATCC 27012, Mycobacterium abscessus, Cryptococcus gattii ATCC 24065, and Cryptococcus neoformans ATCC 24067) demonstrated activity against the bacterium P. aeruginosa ATCC 0030 with inhibition diameter zones (IDZ) of 17.6 ± 0.25 mm in the preliminary screening in solid medium. After fermentation in liquid medium, an IDZ of 19.6 ± 0.46 mm and a minimum inhibitory concentration (MIC) of 0.5 mg/mL were detected. The antibiofilm action was observed with 100% inhibition of biofilm formation at a concentration of 0.250 mg/mL. When the infection curve was prepared, it was observed that the metabolite was effective in protecting the larvae of Tenebrio molitor. The metabolite does not show toxicity for eukaryotic cells. The leishmanicidal activity demonstrated that the metabolite presented a dose-dependent effect on the promastigotes forms of Leishmania amazonensis growth and the estimated IC50/72 h was 71.65 ± 7.4 μg/mL. Therefore, it can be concluded that the metabolite produced by the endophytic bacterium Streptomyces sp. is promising for future use as an alternative strategy against bacterial resistance.

A novel strain of endophytic Streptomyces for the biocontrol of strawberry anthracnose caused by Glomerella cingulata

Anthracnose caused by Glomerella cingulata is one of the most devastating diseases of strawberry in Japan, particularly during its nursery period in the summer. In this study, we aimed to isolate and screen endophytic actinobacteria, to identify potential biocontrol agents capable of suppressing strawberry anthracnose. A total of 226 actinobacteria were successfully isolated from surface-sterilized strawberry tissues. In the first screening, 217 out of 226 actinobacteria isolates were studied for their suppression effect on strawberry anthracnose using a detached leaflet assay. It was discovered that isolates MBFA-172 and MBFA-227 markedly suppressed the development of anthracnose lesions. The efficacy of both isolates was then tested on two-month-old strawberry plug seedlings in a controlled environmental chamber. It was found that isolate MBFA-172 provided consistent disease suppression and was thus selected as a final candidate for further evaluation in a glasshouse experiment. Results showed that the severity as well as incidence rate of strawberry anthracnose was significantly reduced by treatment with isolate MBFA-172 compared with that of untreated control. Accordingly, the disease control efficacy provided by MBFA-172 was statistically comparable to the chemical fungicide propineb. A re-isolation experiment using a spontaneous thiostrepton-resistant mutated strain of isolate MBFA-172 revealed that it efficiently colonized the above-ground tissues of strawberry plants for at least three weeks after spray treatment. Using cultural, morphological, and physiological tests combined with 16S rRNA-based molecular analysis, MBFA-172 was identified as a moderately thermophilic Streptomyces thermocarboxydus-related species. Upon review, our results strongly indicated that MBFA-172 is a promising biocontrol agent for strawberry anthracnose.

Antiplasmodial natural products: an update

Background

Malaria remains a significant public health challenge in regions of the world where it is endemic. An unprecedented decline in malaria incidences was recorded during the last decade due to the availability of effective control interventions, such as the deployment of artemisinin-based combination therapy and insecticide-treated nets. However, according to the World Health Organization, malaria is staging a comeback, in part due to the development of drug resistance. Therefore, there is an urgent need to discover new anti-malarial drugs. This article reviews the literature on natural products with antiplasmodial activity that was reported between 2010 and 2017.

Methods

Relevant literature was sourced by searching the major scientific databases, including Web of Science, ScienceDirect, Scopus, SciFinder, Pubmed, and Google Scholar, using appropriate keyword combinations.

Results and Discussion

A total of 1524 compounds from 397 relevant references, assayed against at least one strain of Plasmodium, were reported in the period under review. Out of these, 39% were described as new natural products, and 29% of the compounds had IC₅₀ ≤ 3.0 µM against at least one strain of Plasmodium. Several of these compounds have the potential to be developed into viable anti-malarial drugs. Also, some of these compounds could play a role in malaria eradication by targeting gametocytes. However, the research into natural products with potential for blocking the transmission of malaria is still in its infancy stage and needs to be vigorously pursued.

Natural Occurrence, Bioactivity and Biosynthesis of Elaiophylin Analogues

Elaiophylins belong to a special family of 16-membered macrodiolides with C₂-symmetry. They have exhibited remarkable biological activities, such as antimicrobial, anthelmintic, anticancer, immunosuppressive, anti-inflammatory, antiviral, and α-glucosidase inhibitory activities. A member of elaiophylins, efomycin M, is as a specific small molecule inhibitor of selectin in preclinical trial for the treatment of psoriasis, ischemia-reperfusion, and allergy. The biosynthetic investigation of elaiophylins has uncovered a unique thioesterase, which is responsible for the formation of C₂-symmetric diolide. We herein summarize the natural occurrence, bioactivity, and biosynthesis of elaiophylins covering the literatures from 1959 to 2019. Hopefully, this review will inspire further research interests of these compounds and encourage the discovery of new analogues by metabolic engineering or genome mining.

Efomycins K and L From a Termite-Associated Streptomyces sp. M56 and Their Putative Biosynthetic Origin

Two new elaiophylin derivatives, efomycins K (1) and L (2), and five known elaiophylin derivatives (3–7) were isolated from the termite-associated Streptomyces sp. M56. The structures were determined by 1D and 2D NMR and HR-ESIMS analyses and comparative CD spectroscopy. The putative gene cluster responsible for the production of the elaiophylin and efomycin derivatives was identified based on significant homology to related clusters. Phylogenetic analysis of gene cluster domains was used to provide a biosynthetic rational for these new derivatives and to demonstrate how a single biosynthetic pathway can produce diverse structures.

Characterisation of Two Polyketides from Streptomyces sp. SKH1-2 Isolated from Roots of Musa (ABB) cv. 'Kluai Sao Kratuep Ho'

An endophytic actinomycete strain SKH1-2 isolated from Musa (ABB) cv. 'Kluai Sao Kratuep Ho' collected in Suphan Buri province (14° 54' 22.5″ N/100° 04' 50″ E), Thailand, was identified as Streptomyces pseudovenezuelae based on phenotypic and chemotaxonomic characteristics, and 16S rRNA sequence analyses. A chemical investigation led to the isolation of two polyketide molecules from the n-butanol crude extract of the strain SKH1-2 culture broth. The compounds were purified using various chromatographic techniques and identified using spectroscopic methods compared with earlier published data. Compound 1, chartreusin, is known as an anti-Gram (+) bacterial compound and was active against Bacillus subtilis ATCC 6633, Kocuria rhizophila ATCC 9341 and Staphylococcus aureus ATCC 6538p with MIC values of 3.1, 1.6 and 12.5 μg/mL, respectively. Compound 2, lumichrome, did not show activity against all tested microbes. To our knowledge, this is the first report of chartreusin and lumichrome isolated from S. pseudovenezuelae. Taken together, it could be proved that Thai plant species are valuable reservoirs of interesting endophytic actinomycetes producing several interesting biologically active compounds.

Biocontrol of Aspergillus flavus on Peanut Kernels Using Streptomyces yanglinensis 3-10

The bacterium, Streptomyces yanglinensis 3-10, shows promise in the control of many phytopathogenic fungi. In this study, S. yanglinensis and its antifungal substances, culture filtrate (CF3-10) and crude extracts (CE3-10), were evaluated for their activity in reducing growth and aflatoxin AFB1 production by Aspergillus flavus, both in vitro and in vivo on peanut kernels. The results showed that in dual culture conditions, S. yanglinensis reduced the mycelial growth of A. flavus about 41% as compared to control. The mycelial growth of A. flavus was completely inhibited on potato dextrose agar amended with CF3-10 at 3% (v/v) or CE3-10 at 2.5 μg/ml. In liquid culture experiments, growth inhibition ranged from 32.3 to 91.9% with reduction in AFB1 production ranging from 46.4 to 93.4% using different concentrations of CF3-10 or CE3-10. For in vivo assays, CF3-10 at 0.133 ml/g (v/w) or CE3-10 at 13.3 μg/g (w/w) reduced the postharvest decay of peanut kernels by inhibiting visible growth of A. flavus leading to an 89.4 or 88.1% reduction in AFB1 detected, respectively. Compared with the controls, CF3-10 and CE3-10 in A. flavus shake culture significantly reduced expression levels of two AFB1 biosynthesis genes, aflR and aflS. Furthermore, electron microscopy observation showed that CF3-10 (2%, v/v) caused hyphae growth to be abnormal and shriveled, cell organelles to degenerate and collapse, large vacuoles to appear. These results suggest that S. yanglinensis 3-10 has potential as an alternative to chemical fungicides in protecting peanut kernels and other agricultural commodities against postharvest decay from A. flavus.

Atmospheric Precipitations, Hailstone and Rainwater, as a Novel Source of Streptomyces Producing Bioactive Natural Products

A cultivation-dependent approach revealed that highly diverse populations of Streptomyces were present in atmospheric precipitations from a hailstorm event sampled in February 2016 in the Cantabrian Sea coast, North of Spain. A total of 29 bioactive Streptomyces strains isolated from small samples of hailstone and rainwater, collected from this hailstorm event, were studied here. Taxonomic identification by 16S rRNA sequencing revealed more than 20 different Streptomyces species, with their closest homologs displaying mainly oceanic but also terrestrial origins. Backward trajectory analysis revealed that the air-mass sources of the hailstorm event, with North Western winds, were originated in the Arctic Ocean (West Greenland and North Iceland) and Canada (Labrador), depending on the altitude. After traveling across the North Atlantic Ocean during 4 days the air mass reached Europe and precipitated as hailstone and rain water at the sampling place in Spain. The finding of Streptomyces species able to survive and disperse through the atmosphere increases our knowledge of the biogeography of genus Streptomyces on Earth, and reinforces our previous dispersion model, suggesting a generalized feature for the genus which could have been essential in his evolution. This unique atmospheric-derived Streptomyces collection was screened for production of bioactive secondary metabolites. Analyses of isolates ethyl acetate extracts by LC-UV-MS and further database comparison revealed an extraordinary diversity of bioactive natural products. One hundred molecules were identified, mostly displaying contrasted antibiotic and antitumor/cytotoxic activities, but also antiparasitic, antiviral, anti-inflammatory, neuroprotector, and insecticide properties. More interestingly, 38 molecules not identified in natural products databases might represent new natural products. Our results revealed for the first time an extraordinary diversity of Streptomyces species in the atmosphere able to produce an extraordinary repertoire of bioactive molecules, thus providing a very promising source for the discovery of novel pharmaceutical natural products.

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants

The fungus-growing ant-microbe symbiosis is an ideal system to study chemistry-based microbial interactions due to the wealth of microbial interactions described, and the lack of information on the molecules involved therein. In this study, we employed a combination of MALDI imaging mass spectrometry (MALDI-IMS) and MS/MS molecular networking to study chemistry-based microbial interactions in this system. MALDI IMS was used to visualize the distribution of antimicrobials at the inhibition zone between bacteria associated to the ant Acromyrmex echinatior and the fungal pathogen Escovopsis sp. MS/MS molecular networking was used for the dereplication of compounds found at the inhibition zones. We identified the antibiotics actinomycins D, X2 and X_0β, produced by the bacterium Streptomyces CBR38; and the macrolides elaiophylin, efomycin A and efomycin G, produced by the bacterium Streptomyces CBR53.These metabolites were found at the inhibition zones using MALDI IMS and were identified using MS/MS molecular networking. Additionally, three shearinines D, F, and J produced by the fungal pathogen Escovopsis TZ49 were detected. This is the first report of elaiophylins, actinomycin X_0β and shearinines in the fungus-growing ant symbiotic system. These results suggest a secondary prophylactic use of these antibiotics by A. echinatior because of their permanent production by the bacteria.

Reveromycins A and B from Streptomyces sp. 3-10: Antifungal Activity against Plant Pathogenic Fungi In vitro and in a Strawberry Food Model System

This study was conducted to determine the antifungal activity of the metabolites from Streptomyces sp. 3–10, and to purify and identify the metabolites. Meanwhile, the taxonomic status of strain 3–10 was re-evaluated. The cultural filtrates of strain 3–10 in potato dextrose broth were extracted with ethyl acetate. The resulting crude extract at 1 and 5 μg/ml inhibited growth of 22 species in 18 genera of plant pathogenic fungi and Oomycetes, accounting for 92% of the total 24 tested species, suggesting that it has a wide antifungal spectrum. Two compounds were purified from the crude extract and were identified as reveromycins A and B, which demonstrated high antifungal activity against Botrytis cinerea, Mucor hiemails, Rhizopus stolonifer, and Sclerotinia sclerotiorum under acidic pH conditions. Both the crude extract and reveromycin A from strain 3–10 at 10, 50, and 100 μg/ml showed high efficacy in suppression of strawberry fruit rot caused by the above-mentioned four pathogens. The efficacy was comparable to that of corresponding commercial fungicides (pyrimethanil, captan, dimetachlone) used in management of these pathogens. Morphological, physiological, and phylogenetic characterization showed that strain 3–10 is closely related to Streptomyces yanglinensis 1307^T, representing a novel phylotype in that species. This study reported a new strain with reveromycins-producing capability. The finding is important for further exploitation of reveromycins for agricultural use.

Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.