Streptomyces: The biofactory of secondary metabolites

Engineering bacterial cell morphology for the design of robust cell factories

Bacteria come in a wide variety of shapes, ranging from spherical or rod-shaped unicellular cells to complex multicellular structures. These shapes have evolved to benefit the organism in its natural environment. However, industry often takes such organisms from their natural environment to produce useful molecules that favor mankind. Their natural morphology is often far from optimal for use in an industrial setting. Filamentous bacteria, for instance, have a morphology that presents unique challenges for industrial settings. Therefore, various engineering approaches have been developed to optimize their morphology. This review explores a spectrum of successful engineering strategies, offering insights and providing inspiration for future advancements. It holds the potential to lead the way in optimizing morphology in challenging microorganisms and thus improve their exploitability in biotechnology.

Morphology-engineered alleviation of mycelial aggregation in Streptomyces chassis for potentiated production of secondary metabolites

The genus Streptomyces exhibits a complex life cycle of morphological differentiation and an extraordinary capacity to produce numerous bioactive secondary metabolites. In submerged cultures, Streptomyces species usually grow in the form of mycelial networks and aggregate into large pellets or clumps, which is generally unfavorable for industrial production. This study aimed to construct efficient microbial cell factories by manipulating morphology-related genes. We herein employed a morphology engineering approach to generate eight engineered derivatives (MECS01∼MECS08) of Streptomyces coelicolor M1146, a versatile chassis widely used for the heterologous production of various secondary metabolites. We found that genetic manipulation of morphology-related genes exerted a substantial influence on the growth and mycelial characteristics of the engineered strains. Once the native actinorhodin gene cluster was introduced into these strains, antibiotic production increased in all engineered strains compared to the parental strain. Notably, a significant elevation of actinorhodin production was observed in three of the engineered strains, MECS01, MECS03 and MECS05. Similar scenarios occurred when expressing the staurosporine gene cluster and the carotenoid gene cluster in these three engineered derivatives, respectively. Our study demonstrates that morphology engineering represents an effective strategy for alleviating mycelial aggregation. It has also expanded the toolkit of Streptomyces chassis available for the heterologous expression of gene clusters encoding a variety of secondary metabolites.

Streptomycetes as a promising source of antimicrobial compounds: A GC-MS-based dereplication study

The extensive microbial resistance to existing antimicrobial medicines presents a significant issue in treating diverse microbial infections, whereas actinomycetes remain a viable source of antimicrobial natural products. We planned to employ gas chromatography-mass spectrometry (GC-MS)-based dereplication analysis to investigate the chemical profile of a bioactive actinomycete. Our actinomycete MFS-I31 demonstrated broad antimicrobial potential against the bacterial pathogens Staphylococcus aureus (ATCC 43300), Listeria monocytogenes (ATCC 7644), Escherichia coli (ATCC 25922), and Salmonella enterica (ATCC 14028), as well as the yeast-like fungus Candida albicans (ATCC 60193). The 16S rRNA gene sequencing of the MFS-I31 isolate exhibited a powerful resemblance to Streptomyces species. The characterization of the major antibacterial compounds in its cell-free supernatant (CFS) revealed good stability at different temperatures ranging from 4 °C to 93 °C, whereas the activity was diminished upon precipitation using ammonium sulphate indicating the proteinaceous nature of the major antimicrobial compounds. Notably, the proton nuclear magnetic resonance (1H NMR) revealed peaks in both aromatic and aliphatic areas, demonstrating the variety of the principal secondary metabolites in the crude extract of Streptomyces sp. MFS-I31. Moreover, the GC-MS-based dereplication research of our actinomycete revealed the richness of its chemical profile with different classes of compounds, including volatile molecules with antimicrobial properties. Finally, the contact bioautography demonstrated the good chance of isolating antimicrobial natural products from Streptomyces sp. MFS-I31 if it would be subjected to chemical isolation work. To summarize, soil Streptomycetes remain a valuable source of many antimicrobial natural compounds, particularly when implementing chemical profiling and dereplication studies.

Effect of Streptomyces spp. metabolites and the combination of biochar and compost on Fusarium graminearum inhibition, triticale growth, and soil properties

Fusarium graminearum is the most harmful pathogen associated with Fusarium Head Blight (FHB) disease in triticale. Among the strategies that can be envisaged for its control, the reuse of organic residues for the production of secondary metabolites from Streptomyces spp. is particularly promising. The study presented herein focuses on the assessment of the antagonistic capacity of the culture filtrates of Streptomyces rochei alone, with compost, with biochar or with both of them, and their culture filtrates against F. graminearum. Firstly, the secondary metabolites were characterized by gas chromatography-mass spectrometry, with 5-Hydroxymethylfurfural, 2-3 Butanediol, Oxime-, methoxy-phenyl and acid butanoic being the most abundant chemical species. Subsequently, the capacity of S. rochei to inhibit the growth of the pathogen was tested in dual culture plate assays, finding 83 % inhibition. Sporangial tests showed that the mixture of S. rochei and biochar can inhibit 100 % of sporangia germination. Micropot trials conducted on triticale using the crop filtrates not only inhibited pathogen growth with all treatments but also improved crop growth. Hence, the culture filtrates of biochar, compost, compost and biochar, and the selected Streptomyces spp. culture filtrates may be put forward as promising protection treatments for the sustainable control of fusariosis.

Isolation of Streptomyces spp. Exhibiting Potent Antibiofilm Activity Against Clinically Isolated Bacterial Strains

The increasing threat of antimicrobial resistance (AMR) highlights the urgent need for alternative therapeutic strategies, particularly those targeting microbial virulence factors like biofilm formation. This study aimed to isolate and identify Streptomyces species with potential antibiofilm activity against clinically relevant biofilm-producing bacterial pathogens. Actinomycetes were isolated from soil samples, cultured on Gause's synthetic agar (GSA) and identified through 16S rRNA gene sequencing. Clinically isolated pathogenic bacteria, including Proteus mirabilis, Escherichia coli, Klebsiella oxytoca, Acinetobacter baumannii, and Klebsiella pneumoniae, were identified using the VITEK 2 system. The antibiofilm and antibacterial activities of the bioactive compounds extracted from Streptomyces spp. were assessed using the agar plug diffusion method and quantitative biofilm assays with crystal violet staining. Among the isolated Streptomyces strains, Streptomyces albogriseolus was identified as a promising producer of bioactive metabolites. The isolate exhibited 99% similarity to strain NBRC 3709 based on 16S rRNA gene sequencing. The crude extract at a concentration of 20 mg/mL demonstrated significant antibacterial activity, with inhibition zones of 11.9 mm against K. pneumoniae and 15.1 mm against E. coli. Moreover, the extract significantly reduced biofilm formation in A. baumannii and E. coli. A lower antibiofilm effect was also observed against K. pneumoniae, P. mirabilis, and K. oxytoca, with K. oxytoca exhibiting the weakest biofilm inhibition. In conclusion, secondary metabolites from S. albogriseolus display significant antibiofilm activity against drug-resistant pathogens, with efficacy varying by bacterial species and extract concentration. These findings underscore the potential of Streptomyces-derived metabolites as promising candidates for combating biofilm-associated infections. Further studies are recommended to explore their mechanism of action and optimize their potential therapeutic application.

A CRISPR-Cas9 system for knock-out and knock-in of high molecular weight DNA enables module-swapping of the pikromycin synthase in its native host

BACKGROUND

Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA.

RESULTS

We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI-pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin.

CONCLUSION

Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.

Genomic analysis and process optimization for nigericin production in a newly-isolated antimicrobial Streptomyces

Streptomyces, the dominant species of actinomycetes, contribute to a large proportion of bioactive natural products. In our previous study, over 2400 culture extracts were subjected to bioassays against Candida albicans and Staphylococcus aureus. Among these, Streptomyces javensis named Inha503, was found to produce nigericin, which exhibits antimicrobial activity against gram-positive bacteria, such as Micrococcus luteus and S. aureus. This study aimed to understand the genomic features of S. javensis Inha503 and optimize the downstream process to improve the titer of nigericin derivatives. Identification of the nigericin biosynthetic gene cluster (BGC) in the chromosome was confirmed using whole-genome bioinformatics and core BGC knockout results. The cultivation time was optimized to 10 days, and nigericin derivatives were identified and quantified using LC/MS. Among the seven-production media for Streptomyces, the highest production of nigericin was obtained in the R5 medium, which exhibited a 1.75-fold increase compared to the previous conditions. Additionally, the nigericin extraction process was optimized using ethyl acetate as a single solvent and a mixture of ethyl acetate and ethanol in a 7:3 ratio. The highest titer of nigericin derivatives were obtained in R5 medium after 10 days with extraction using a mixture of ethyl acetate and ethanol, implying that optimized purification processes with genetic insights of S. javensis Inha503 as a promising platform for bioactive compound production such as nigericin.

Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains

Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.

Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum

BACKGROUND

Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.

RESULTS

Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.

CONCLUSIONS

Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.

Borrelidin M: a new borrelidin derivative obtained from Streptomyces rochei VL-16 exhibited potent antibacterial and antiproliferative properties

The lookout for novel metabolites to overcome the threat imposed by antibiotic resistant pathogens is on the rise globally. The present study reports on the identification and characterisation of a new borrelidin derivative from Streptomyces rochei VL-16 strain that was isolated from the soil samples of Osudu Lake in Puducherry. The active compound produced by Streptomyces rochei VL-16 strain was purified sequentially by thin layer, column and high performance liquid chromatography techniques. The purified compound was subsequently identified as borrelidin through Q-TOF-HR-LCMS, FTIR and UV-Vis spectroscopy techniques. Based on integration proton NMR signals and HR-ESI-MS peak pattern, the compound was further identified as a new derivative of borrelidin. Its 3D structure was optimised using density functional theory. The new derivative obtained in this study was designated as borrelidin M (C28H41NO5, Mol. wt.471.3 g/mole). This derivative was found to exhibit potent inhibitory effects against the foodborne pathogens including Clostridium perfringens, Aeromonas hydrophila, Staphylococcus aureus, Listeria monocytogenes and Yersinia enterocolitica. Also, borrelidin M exhibited anticancer and anti-metastatic effects against A549 cell line with an IC50 value of 17.5 μM. Collectively, these findings indicated promising biomedical applications of this new derivative of borrelidin.

Biological activity of secondary metabolites of actinomycetes and their potential sources as antineoplastic drugs: a review

Actinomycetes are an important group of Gram-positive bacteria, renowned for their ability to produce a wide array of structurally diverse and biologically active secondary metabolites. These secondary metabolites have significant applications in fields such as antimicrobial and antifungal treatments and show tremendous potential in cancer research. To comprehensively review the antitumor potential of actinomycetes-derived secondary metabolites, we conducted a systematic literature search across PubMed, Web of Science, and Scopus databases, covering the period from January 2019 to January 2024. The search used keywords including "actinomycetes," "secondary metabolites," "antitumor," "cancer therapy," "bioactivity," and "clinical application." A total of 95 relevant articles were identified through database searches. After applying inclusion and exclusion criteria, 87 articles were deemed eligible and fully reviewed in this article. These studies highlighted diverse structural classes of actinomycetes-derived antitumor compounds, including polyketides, non-ribosomal peptides, alkaloids, and terpenoids. Many of these metabolites exhibit potent anticancer properties through mechanisms such as inducing apoptosis, inhibiting proliferation, disrupting tumor microenvironment, and targeting key oncogenic signaling pathways. This review underscores the crucial role of actinomycetes secondary metabolites as an invaluable resource for antitumor drug discovery, offering new scientific insights into natural product-based cancer therapies, expanding the molecular toolbox for clinical oncology, and ultimately contributing to public health by advancing effective and innovative treatment options for cancer patients.

Genome Mining Reveals Rifamycin Biosynthesis in a Taklamakan Desert Actinomycete

Actinomycetes are recognized for producing diverse bioactive natural products, yet most biosynthetic gene clusters (BGCs) remain inactive under laboratory conditions. Rare actinomycetes from extreme environments represent underexplored reservoirs of metabolic potential. This study investigates Actinomadura sp. TRM71106, a rare actinomycete isolated from the Taklamakan Desert, through integrated genomic and metabolomic approaches. Genome sequencing revealed 45 secondary metabolic BGCs, including BGC38 showing 65% nucleotide similarity to the rifamycin BGC. Gene cluster networking and linear comparisons predicted its capacity to encode novel rifamycin analogs. Targeted activation strategies-overexpression of the pathway-specific regulator LuxR combined with metabolite isolation-mark the first activation of a rifamycin-like BGC in desert actinomycetes. This study highlights the untapped biosynthetic potential of rare actinomycetes in extreme environments and establishes Actinomadura sp. TRM71106 as a novel source for rifamycin production. These results provide a promising avenue for expanding the clinical pipeline of rifamycin-derived antibiotics.

Streptomyces flavusporus sp. nov., a Novel Actinomycete Isolated from Naidong, Xizang (Tibet), China

The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. A Gram-positive, pink-pigmented Streptomyces strain designated HC307T was isolated from a soil sample collected in Xizang (Tibet), China. The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. In this study, the 16S rRNA sequence of strain HC307T exhibited the highest similarity with Streptomyces prasinosporus NRRL B-12431T (97.5%) and Streptomyces chromofuscus DSM 40273T (97.3%), which were below 98.7%. The draft genome of the bacteria was 10.0 Mb, with a G+C content of 70.0 mol%. The average nucleotide identity (ANI) values of strain HC307T and similar type strains ranged from 78.3% to 87.5% (<95%). The digital DNA-DNA hybridization (dDDH) values ranged from 22.6% to 33.9% (<70%), which was consistent with the results obtained from phylogenetic tree analysis. Phenotypically, this bacterium grew within the temperature range of 25-40 °C, at a pH range of 5 to 9, and in NaCl concentrations from 0% to 6% (w/v). The polar lipid profile of strain HC307T was diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The analysis of 32 biosynthetic gene clusters (BGCs) indicated the strain's capacity to synthesize diverse compounds. Phylogenetic and phenotypic analyses demonstrated that strain HC307T represented a novel species within the genus Streptomyces, and proposed the name Streptomyces flavusporus sp. nov., with strain HC307T (=DSM 35222T=CGMCC 32047T). The strain was deposited in Deutsche Sammlung von Mikroorganismen und Zellkulturen and the China General Microbiological Culture Collection Center for patent procedures under the Budapest Treaty.

A review on the expanding biotechnological frontier of Pedobacter

The genus Pedobacter consists of Gram-negative bacteria with a broad geographic distribution, isolated from diverse habitats, including water, soil, plants, wood, rocks and animals. However, characterization efforts have been limited to a small number of species. Likewise, in the context of natural products (NP), only a small fraction of Pedobacter -derived NPs have been characterized so far. In contrast, in silico analysis of the increasing number of available genomes in the databases, suggests a wealth of yet to be discovered compounds. Notable biotechnological applications described so far include the production of heparinases and chondroitinases for therapeutic purposes, phytases and galactosidases as aquaculture feed supplements, alginate lyases for biofuel production, and secondary metabolites such as pedopeptins and isopedopeptins with antimicrobial properties. Further research integrating synthetic biology approaches, holds great promise for unlocking the hidden potential of members of this genus, thus expanding its industrial applications.

Ibrahim HI. 2-Amino-3-Chlorobenzoic Acid from Streptomyces coelicolor: A Cancer Antagonist Targeting PI3K/AKT Markers via miRNA Modulation

Background/Objectives: Actinomycetes, particularly species within the Streptomyces genus, are renowned for their ability to produce a wide array of bioactive molecules with therapeutic potential. This study aimed to comprehensively investigate the antimicrobial and anticancer properties of Streptomyces coelicolor ERI-15, with a particular focus on a purified compound, 2-amino-3-chlorobenzoic acid (2A3CB), and its efficacy against microbial pathogens and breast cancer cell lines. Methods: Antimicrobial compounds were produced through fermentation techniques and isolated via column chromatography. Bioassay-guided fractionation was conducted against Staphylococcus aureus (ATCC 25923), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (ATCC 25922), and Bacillus subtilis (ATCC 441). Major fractions were further purified using preparative thin-layer chromatography (TLC). The structures of active compounds were elucidated using spectral analyses including IR, mass spectrometry, and 1H/13C NMR. The compound 2A3CB (m/z 171) was tested against MDA-MB-231 and 3T3 cell lines. Cytotoxicity was assessed by the MTT assay, and apoptotic mechanisms were explored via cell proliferation assays, dual fluorescent staining, migration and invasion assays, and analysis of apoptotic markers at mRNA and protein levels. Results: 2A3CB exhibited strong cytotoxic effects on MDA-MB-231 cells, with IC50 values of 26 µM, 5 µM, and 7.2 µM at 24, 48, and 72 h, respectively. It significantly inhibited cell proliferation and migration, and induced apoptosis via caspase-mediated pathways. Expression levels of PTEN, PCNA, BAX, and STAT3 were downregulated, suggesting inhibition of metastasis through the suppression of invasion and migration. Conclusions: The results demonstrate that 2A3CB, derived from S. coelicolor ERI-15, possesses potent antimicrobial and anticancer properties. Its ability to inhibit growth and induce apoptosis in MDA-MB-231 breast cancer cells highlights its potential as a natural therapeutic candidate for targeted cancer treatment, particularly in breast cancer progression.

Impact of altitudinal variations on plant growth dynamics, nutritional composition, and free living rhizospheric N2 fixing bacterial community of Eruca sativa

High-altitude environments present unique abiotic stresses, yet their impact on the growth, nutritional quality, and rhizospheric interactions of E. sativa remains underexplored. Here, we investigate the altitudinal variations in growth dynamics, nutritional composition, and rhizospheric free-living N2-fixing bacteria (NFBs) of E. sativa (Arugula) grown at higher (3,524 m, Leh-Ladakh) and lower (321 m, Chandigarh) altitudes. Results revealed significant physiological adaptations to high-altitude conditions, with increased concentrations of magnesium (748.84 ± 4.06 mg/100 g), iron (189.83 ± 2.16 mg/100 g), and manganese (8.48 ± 0.27 mg/100 g), while potassium (3,400.83 ± 3.82 mg/100 g), sodium (175.83 ± 1.44 mg/100 g), and copper (1.69 ± 0.01 mg/100 g) were higher at lower-altitude. Zinc content remained unchanged. Notably, dietary nitrate was higher (155.67 ± 22.12 mg/100 g) at high-altitudes. Rhizospheric NFBs were isolated and functionally characterized for N2-fixation efficacy along with various plant growth-promoting (PGP) attributes; viz., production of ammonia, siderophores, HCN, IAA and phosphate solubilization. Field inoculation with selected strains significantly enhanced nitrogen content and plant growth. Soil chemical analysis further revealed significant differences between the altitudes. A total of twenty-seven NFBs belonging to Actinobacteria (77%), Proteobacteria (11%), Firmicutes(8%), and Bacteroidetes(4%) were isolated, with Streptomyces being the predominant genus, exhibiting distinct species at different altitudes. Remarkably, high-altitude strains showed significantly higher N2-fixing efficiencies (88.15 ± 17.41 µgN mL-1) than lower-altitude (65.7 ± 14.36 µgN mL-1) along with superior PGP traits. Overall, these findings suggest that E. sativa, enriched in key nutrients at high-altitudes, could be a valuable functional food crop, addressing the dietary needs of high-altitude populations. Furthermore, the rhizospheric NFBs identified in this study may be potentially beneficial for the development of novel bio-fertilizers, promoting eco-friendly agricultural practices through improved N2-fixation. Further field trials are recommended to validate their potential for sustainable crop production.

Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources

Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.

Secondary Metabolites from Bacillus spp. probiotics as potential treatments for multidrug-resistant pathogens: A comprehensive review

The discovery of antibiotics is a significant medical breakthrough, saving millions of lives. However, the widespread misuse and overuse of antibiotics led to the development of antimicrobial resistance. Spore-forming probiotics from Bacillus spp. show great interest as antimicrobial agents through the production of strain-specific bioactive secondary metabolites. This review summarizes the broad-spectrum antimicrobial activities of Bacillus spp. secondary metabolite groups and their reported mechanisms of action, underscoring the urgency in developing novel antimicrobial drugs.

Editorial for the Special Issue "Microbial Diversity and Microbial Resistance"

In the beginning, it was diversity-or so evolutionary biology suggest when interpreting how and why antibiotic production began on Earth [...].

Novel Insights and Genomic Characterization of Coral-Associated Microorganisms from Maldives Displaying Antimicrobial, Antioxidant, and UV-Protectant Activities

Coral reef survival is crucial for the socio-ecological interest of many countries, particularly for the Republic of Maldives, whose reef integrity influences the country's livelihoods and economy. These ecosystems are being severely impacted by multiple stressors, leading to declines in biodiversity. In the last few decades, researchers have focused on studying coral-associated microorganisms (CAMs) and their symbiotic role in coral health and resilience. Metabarcoding analysis has been widely utilized to study CAM diversity under various conditions but provides limited information on their functional roles. Therefore, cultivation of bacterial strains remains indispensable for validating ecological and biotechnological hypotheses. In this study, we investigated the microbial community associated with two abundant corals in Maldives, Porites lobata and Acropora gemmifera, and evaluated the antimicrobial, antioxidant, and UV-protectant properties of 10 promising isolated strains. The selected CAMs, Pseudoalteromonas piscicida 39, Streptomyces parvus 79, Microbacterium sp. 92 (a potential novel species), and Micromonospora arenicola 93, exhibited antibiotic activity against a panel of pathogenic strains (MIC from 0.01 to 500 µg/mL), antioxidant (comparable effect to that of Trolox and ascorbic acid), and UV-screen activities (protection of human keratinocytes at 200 µg/mL). Genomes revealed their dual potential in contributing to coral restoration and drug discovery strategies. These findings highlight the biotechnological relevance of CAMs, representing an important step toward the identification of novel and bioactive bacterial species beneficial for coral reef ecosystems and human health.

Diversified Soil Types Differentially Regulated the Peanut (Arachis hydropoaea L.) Growth and Rhizosphere Bacterial Community Structure

Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and bacterial structure of rhizosphere soil in acidic (AT), neutral (NT), and saline-alkali (ST) soils, elucidating the internal relationship between soil type and peanut yield. Our results showed that different soil types exhibited significant differences in peanut yield, with ST demonstrating the lowest yield per plant, showing an 85.05% reduction compared to NT. Furthermore, available phosphorus content, urease, and invertase activities were substantially reduced in both ST and AT, particularly in ST by 95.35%, 38.57%, and 62.54%, respectively. Meanwhile, metagenomic sequencing unveiled a notable decline in Bradyrhizobium and Streptomyces in these soils, which is crucial for soil improvement. Further metabolic pathway analysis revealed that the reduction in pathways related to soil remediation, fertility improvement, and stress response in AT and ST may lead to slower peanut growth. In conclusion, peanuts cultivated in acidic and saline-alkali soils can increase yield via implementing soil management practices such as improving soil quality and refining micro-environments. Our study provides practical applications for enhancing peanut yield in low- to medium-yield fields.

Bioactive Fraction of Streptomyces thinghirensis MSA1 Effectively Inhibits Biofilm Forming Clinically Significant AMR Pathogens

The escalating threat of antibiotic-resistant microorganisms necessitate the discovery of novel antibacterial agents. This study explores the potential of marine-associated actinomycetes, focusing on Streptomyces thinghirensis MSA1, isolated from the marine sponge Callyspongia diffusa in Palk Bay, India, for its notable antibacterial properties. To optimize the production of bioactive compounds of S. thinghirensis MSA1, we established optimal growth conditions (30 °C, pH 7, 2% salinity, 9-day incubation) and utilized ISP4 medium for enhanced secondary metabolite production. The extracted compound, MSA1, was analyzed through FTIR and GCMS, identifying 20 biologically active components. MSA1 demonstrated potent antibacterial activity against significant pathogens, including Escherichia coli, Klebsiella pneumoniae, Salmonella typhi, Pseudomonas aeruginosa, and MRSA, alongside remarkable antioxidant and anti-biofilm properties. These findings highlight the potential of MSA1 as a promising candidate for developing treatments against antibiotic-resistant infections. This study acknowledges the preliminary nature of the findings and the necessity for further in vivo and clinical trials to fully ascertain the therapeutic potential of MSA1. This research opens avenues for novel antibacterial agents in the fight against antibiotic resistance, underscoring the value of marine biodiversity in medical science.

Separation and identification of nematicidal active compounds in culture filtrate of Streptomyces aquilus JXGZ01 based on metabolomic analysis

BACKGROUND

Meloidogyne incognita is one of the pathogenic nematodes with the widest range and most serious damage, which can infest many food and cash crops. We screened a strain of Streptomyces aquilus JXGZ01, whose culture filtrate showed excellent nematicidal activity and egg hatching inhibition activity against M. incognita. In this study, we performed metabolomic analysis of the culture filtrate of this strain.

RESULTS

The data showed that of the total 304 differential metabolites, 244 were significantly up-regulated and 60 were significantly down-regulated. Seven compounds with large fold changes were selected from the up-regulated metabolites to test the nematicidal activity against M. incognita. The mortality of M. incognita in both 5 and 10 mg mL-1 of 4-acetylaminobutyric acid was more than 85%. The mortality of M. incognita in both 10 and 100 mg mL-1 of (R)-(-)-2-phenylglycinol was more than 70%. The mortality rate of M. incognita in 100 mg of N-acetyl-l-glutamic acid was 78.25%. In addition, the hatching inhibition rate of egg masses were more than 90% for both 5 and 10 mg mL-1 of 4-acetylaminobutyric acid. The hatching inhibition rate of egg masses were more than 80% for 100 mg and 10 mg (R)-(-)-2-phenylglycinol. The hatching inhibition rate of 100 mg N-acetyl-l-glutamic acid on eggs was 93.47%.

CONCLUSION

The results demonstrate that S. aquilus can be a candidate microorganism for the biological control of M. incognita, and its metabolites 4-acetylaminobutyric acid and (R)-(-)-2-phenylglycinol had great potential as nematicides. © 2025 Society of Chemical Industry.

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).

A CRISPR-Cas9 System for Knock-out and Knock-in of High Molecular Weight DNA Enables Module-Swapping of the Pikromycin Synthase in its Native Host

Background

Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA.

Results

We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI-pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin.

Conclusion

Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.

A Novel Benzopyrone Derivative from Streptomyces chrestomyceticus ADP4 Inhibits Growth and Virulence Factors of Candida albicans

Antimicrobial resistance (AMR) poses a serious threat to human health globally. Expeditious discovery and development of new drugs has become indispensable for addressing this challenge. In this context, a novel benzopyrone derivative, designated as 82B1, has been isolated from S. chrestomyceticus strain ADP4. This compound exhibited significant inhibitory activity against different Candida species including C. albicans, C. tropicalis, C. krusei, C. parapsilosis and C. auris with minimum inhibitory concentration (MIC90) values in the concentration range of 25-125 µg/mL. The structure of 82B1 was elucidated through analyses of the spectral data obtained using liquid chromatography-tandem mass spectrometry (LCMS/MS), Nuclear Magnetic Resonance (NMR), Fourier Transform Infrared Spectroscopy (FTIR) and Ultraviolet (UV) spectroscopy, that led to its identity as 7, 13, 14-trihydroxy-6H-benzo-[c]-chromen-6-one8-[1'β-carboxycyclopentanyl]-2'β-[8'β-ethylcyclopentane]. It significantly inhibited the major virulence factors of C. albicans such as yeast to hyphae transition, biofilm formation, and secretion of hydrolytic enzymes at its subinhibitory concentrations. It did not display cytotoxicity on human hepatoblastoma cell line (HepG2 cells), signifying its potential as a candidate for anti-Candida drug development.

Unlocking the microbial treasure trove: advances in Streptomyces derived secondary metabolites in the battle against cancer

Streptomyces is widely recognized as the "biological factory" of specialized metabolites comprising a huge variety of bioactive molecules with diverse chemical properties. The potential of this Gram-positive soil bacteria to produce such diversified secondary metabolites with significant biological properties positions them as an ideal candidate for anticancer drug discovery. Some of the Streptomyces-derived secondary metabolites include siderophores (enterobactin, desferrioxamine), antibiotics (xiakemycin, dinactin) pigments (prodigiosin, melanin), and enzymes (L-methioninase, L-asperginase, cholesterol oxidase) which exhibit a pronounced anticancer effect on both in vitro and in vivo system. These secondary metabolites are endowed with antiproliferative, pro-apoptotic, antimetastatic, and antiangiogenic properties, presenting several promising characteristics that make them suitable candidates in the battle against this deadly disease. In this comprehensive review, we have dived deep and explored their history of discovery, their role as anticancer agents, underlying mechanisms, the approaches for the discovery of anticancer molecules from the secondary metabolites of Streptomyces (isolation of Streptomyces, characterization of bacterial strain, screening for anticancer activity and determination of in vitro and in vivo toxicity, structure-activity relationship studies, clinical translation, and drug development studies). The hurdles and challenges associated with this process and their future prospect were also illustrated. This review highlights the efficacy of Streptomyces as a "microbial treasure island" for novel anticancer agents, which warrants sustained research and exploration in this field to disclose more molecules from Streptomyces that are unidentified and to translate the clinical application of these secondary metabolites for cancer patients.

Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution

Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.

Microbiome profiling and Actinomycetes isolation from tropical marine sponges

Marine sponges are well-known for their production of bioactive compounds, many of which are synthesized by their associated symbiotic microorganisms. Among these, Actinomycetes are of particular interest due to their ability to produce secondary metabolites with antimicrobial and antitumor activities. We aimed to investigate the bacterial microbiome of tropical marine sponges, with an emphasis on the diversity and distribution of Actinomycetes, employing both culture-dependent and culture-independent approaches. Five sponge samples (PF01-PF05) were collected from Sichang Island, Chonburi Province, Thailand. The bacterial communities were analyzed using 16S rRNA gene sequencing and bioinformatics tools, revealing a significant microbial diversity dominated by Cyanobacteria, Actinomycetota, and Chloroflexi. Notably, PF01 (Penares nux) exhibited the highest microbial diversity, while PF05 (Cacospongia sp.) had the lowest. Actinomycetes, particularly the genus Micromonospora, were successfully isolated from all samples, with PF03 (Ircinia mutans) yielding the highest number of strains. Culture-independent analysis identified a greater proportion of unculturable Actinomycetes compared to those isolated through traditional methods, underscoring the limitations of culture-dependent techniques. This study enhances our understanding of sponge-associated microbial diversity and highlights the potential for isolating Actinomycetes from these sponges for novel drug discovery and other bioprospective applications.

Genomic Insights and Antimicrobial Potential of Newly Streptomyces cavourensis Isolated from a Ramsar Wetland Ecosystem

The growing threat of antimicrobial resistance underscores the urgent need to identify new bioactive compounds. In this study, a Streptomyces strain, ACT158, was isolated from a Ramsar wetland ecosystem and found to exhibit broad-spectrum effects against Gram-positive and Gram-negative bacteria, as well as fungal pathogens. The active strain was characterized as S. cavourensis according to its morphology, phylogenetic analysis, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH). Whole-genome sequencing (WGS) and annotation revealed a genome size of 6.86 Mb with 5122 coding sequences linked to carbohydrate metabolism, secondary metabolite biosynthesis, and stress responses. Genome mining through antiSMASH revealed 32 biosynthetic gene clusters (BGCs), including those encoding polyketides, nonribosomal peptides, and terpenes, many of which showed low similarity to known clusters. Comparative genomic analysis, showing high genomic synteny with closely related strains. Unique genomic features of ACT158 included additional BGCs and distinct genes associated with biosynthesis pathways and stress adaptation. These findings highlight the strain's potential as a rich source of bioactive compounds and provide insights into its genomic basis for antimicrobial production and its ecological and biotechnological significance.

Harnessing Biocontrol Potential of Streptomyces rochei Against Pythium aphanidermatum: Efficacy and Mechanisms

Tomato (Solanum lycopersicum) and chilli (Capsicum annuum) are globally significant vegetable crops susceptible to damping-off disease caused by Pythium aphanidermatum, leading to substantial yield losses. The study aimed to document the biocontrol and plant growth promotion potential of Streptomyces rochei against damping-off disease in tomato and chilli. The actinobacterial isolates ACS18 followed by ACT30, and AOE12 were accomplished as the most effective antagonists against P. aphanidermatum in vitro. Molecular characterization confirmed these isolates as members of Streptomyces genus, with ASH 18 the top performer identified as S. rochei isolate. Analysis of biomolecule through GC-MS during ditrophic interaction between pathogen and S. rochei showed the presence of various antifungal metabolites which were directly related to suppression of the pathogen. Subsequently, S. rochei was formulated into a talc-based preparation and used as seed treatment and soil application against damping-off. In greenhouse trials, significant reductions in damping-off incidence were observed, Furthermore, seedlings treated with S. rochei displayed enhanced root and shoot lengths compared to the uninoculated controls. These benefits potentiate S. rochei as a promising biocontrol agent and demonstrating its dual benefits of disease suppression and promotion of seedling growth.

Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in Streptomyces bacteria

Ribosomally synthesized post-translationally modified peptides (RiPPs) are a novel category of bioactive natural products (NPs). Streptomyces bacteria are a potential source of many bioactive NPs. Limited opportunities are available to characterize all the bioactive NP gene clusters. In this study, 410 sequences of Streptomyces were analyzed for RiPPs through genome mining using the National Center for Biotechnology Information (NCBI), by combining BAGEL and anti-SMASH. A total of 4098 RiPPs were found; including both classified (lanthipeptide, RiPP-like, bacteriocin, LAPs, lassopeptide, thiopeptides) and nonclassified RiPPs. Soil was identified as a rich habitat for RiPPs. These data may offer alternative future remedies for various health issues.

Structure, Function, and Biosynthesis of Siderophores Produced by Streptomyces Species

Since the natural supply of iron is low, microorganisms acquire iron by secreting siderophores. Streptomyces is known for its abundant secondary metabolites containing various types of siderophores, including hydroxamate, catecholate, and carboxylate. These siderophores are mainly synthesized through the nonribosomal peptide synthase (NRPS) and non-NRPS pathways and are regulated by ferric uptake regulator and diphtheria toxin regulators. Although both NRPS and non-NRPS pathways adenylate substrates, they differ significantly in the catalytic logic. Siderophores produced by Streptomyces play important roles in fields of agriculture, medicine, and environment. However, their structure, function, and synthetic mechanisms have been inadequately summarized. Therefore, this Review aimed to provide an overview of the classification, structure, biosynthesis, regulation, and applications of siderophores produced by Streptomyces. Finally, the need for a comprehensive and well-defined mechanism for synthesizing siderophores from Streptomyces was highlighted to further promote their commercialization and application in agriculture, medicine, and other areas.

Diversity of secondary metabolites from marine Streptomyces with potential anti-tubercular activity: a review

The bacterial genus Streptomyces is known for the prolific production of secondary metabolites, which exhibit remarkable structural diversity and potent biological activities. Tuberculosis (TB) remains a formidable global health challenge exacerbated by the emergence of antimicrobial resistance (AMR), necessitating the discovery of novel therapeutic agents. The untapped potential of marine Streptomyces-derived secondary metabolites offers a promising avenue for screening anti-tubercular (anti-TB) compounds with unique chemical structures and potential bioactive properties. The review emphasizes the diverse marine habitats and Streptomyces with novel anti-TB bioactive metabolites. It discusses fermentation and bioprocessing strategies for screening anti-TB drugs. This review also covers the chemical diversity, potency, mechanism of action, and structures of about seventy anti-TB compounds discovered from marine Streptomyces. These compounds span various chemical classes, including quinones, macrolactams, macrolides, phenols, esters, anthracyclines, peptides, glycosides, alkaloids, piperidones, thiolopyrrolones, nucleosides, terpenes, flavonoids, polyketides, and actinomycins. It emphasizes the need to explore marine ecosystems to discover more novel anti-TB natural products.

Molecular structural arrangement in quorum sensing and bacterial metabolic production

Quorum sensing (QS) regulates bacterial behaviors such as biofilm formation, virulence, and metabolite production through signaling molecules like acyl-homoserine lactones (AHLs), peptides, and AI-2. These signals are pivotal in bacterial communication, influencing pathogenicity and industrial applications. This review explores the molecular architecture of QS signals and their role in metabolite production, emphasizing structural modifications that disrupt bacterial communication to control virulence and enhance industrial processes. Key findings highlight the development of synthetic QS analogs, engineered inhibitors, and microbial consortia as innovative tools in biotechnology and medicine. The review underscores the potential of molecular engineering in managing microbial behaviors and optimizing applications like biofuel production, bioplastics, and anti-virulence therapies. Additionally, cross-species signaling mechanisms, particularly involving AI-2, reveal new opportunities for regulating interspecies cooperation and competition. This synthesis aims to bridge molecular insights with practical applications, showcasing how QS-based technologies can drive advancements in microbial biotechnology and therapeutic strategies.

Olikomycin A-A Novel Calcium-Dependent Lipopeptide with Antibiotic Activity Against Multidrug-Resistant Bacteria

Research into new antibiotics is becoming increasingly important as antibiotic resistance increases worldwide. The genus Streptomyces in particular is able to produce a wide range of antimicrobial products due to the large number of biosynthetic gene clusters (BGCs) in its genome. However, not all BGCs are expressed under laboratory conditions. In this work, deletion of the gene wblA, encoding a global regulator of natural product biosynthesis and morphogenesis in Streptomyces, led to the production of a novel natural product, olikomycin A, in Streptomyces ghanaensis ATCC 14672. Complete structure elucidation revealed that olikomycin A belongs to a class of calcium-dependent antibiotics known as non-ribosomal peptide synthetase (NRPS)-encoded acidic lipopeptides. These compounds exhibit remarkable antimicrobial activity in the presence of calcium. Insights into olikomycin A biosynthesis were provided by whole genome sequencing and gene inactivation studies, while bioactivity assays showed strong inhibition of the growth of multidrug-resistant Gram-positive pathogens via disrupting cell membrane integrity. Olikomycin A shows an antibiotic profile similar to that of daptomycin, which is already in clinical use.

Biphenyl and Dibenzofuran Phytoalexins Differentially Inhibit Root-Associated Microbiota in Apple, Including Fungal and Oomycetal Replant Disease Pathogens

Apple replant disease (ARD) is a serious soilborne disease in apple nurseries and orchards worldwide. ARD is the result of an unbalanced soil microbiome in which multiple soilborne plant-pathogenic fungi, oomycetes, and nematodes form a disease complex. Biphenyl and dibenzofuran phytoalexins are found in greater quantities in the roots of apple plants grown in ARD soil compared with disinfected ARD soil. However, the contribution of these compounds to plant health or disease is not yet understood. Here, the antimicrobial activity of 14 chemically synthesized biphenyl and dibenzofuran phytoalexins was tested against eight selected microorganisms isolated from either rhizosphere soils or apple roots. These included five potentially beneficial bacteria (Rhodococcus pseudokoreensis strain R79T, R. koreensis strain R85, Streptomyces pulveraceus strain ES16, S. ciscaucasicus GS2, and Priestia megaterium strain B1), two ARD fungal pathogens (Ilyonectria robusta H131 and Dactylonectria torresensis N3), and one oomycete (Globisporangium terrestre). Two phytoalexin mixtures reflecting the percentages of the individual compounds inside the roots (mixture A) and the root exudate (mixture B) were also tested. The two phytoalexin mixtures demonstrated higher antimicrobial activity than the individual phytoalexins, suggesting a synergistic effect. The minimum inhibitory concentration and the half-maximal effective concentration values determined to be active against the eight microbes were within a range of 2.5-fold the ecologically relevant phytoalexin concentration (approximately 33 and 24 µg ml-1 in roots and exudate, respectively). The results contribute to our understanding of the impact of apple root phytoalexins on ARD and suggest potential strategies for disease management.

Draft genome dataset of Streptomyces griseoincarnatus strain R-35 isolated from tidal pool sediments

The marine isolate, Streptomyces griseoincarnatus strain R-35, was isolated from marine sediments collected from the Glencairn Tidal Pool, Table Mountain National Park, Cape Town, South Africa. The genomic DNA was sequenced using the Ion Torrent GeneStudio™ S5 platform, and the de novo assembly was performed using the SPAdes assembler on the Centre for High Performance Computing (CHPC) Lengau Cluster located at the CSIR, Rosebank, South Africa. The draft genome assembly consisted of 722 contigs totaling 7,625,174 base pairs and a G+C% content of 72.2 mol%. Genome completeness and genome contamination were determined as 99.12% and 0.92%, respectively. Genome annotations performed using the Rapid Annotation with Subsystem Technology (RAST) and the Bacterial and Viral Bioinformatics Resource Centre (BV-BRC) determined the presence of 7996 coding sequences (CDS), 63 transfer RNAs (tRNAs), and six ribosomal RNAs (rRNAs). A total of 2570 hypothetical proteins were assigned, and 5246 proteins were assigned to function. The phylogenomic positioning of S. griseoincarnatus strain R-35 was determined using the Type Strain Genome Server (TYGS) and was found to be related to S. griseoincarnatus JCM 4381T, with a digital DNA-DNA hybridisation (dDDH) value of 84.1%, and an OrthoANIu value of 98.22%. The CARD RGI algorithm on Proksee predicted the presence of 6,107 antimicrobial resistance (AMR) features, 27 biosynthetic gene clusters (BGCs) were predicted using antiSMASH, while 189 carbohydrate-active enzymes (CAZymes) were predicted using dbCAN3. The raw genome sequencing data has been submitted to the National Center for Biotechnology (NCBI) under the BioProject ID PRJNA1129156 (BioSample ID Accession Number: SAMN42145163; Short Read Archive (SRA) Accession: SRR29633055; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1129156).

Mitigating genetic instability caused by the excision activity of the phiC31 integrase in Streptomyces

Over the past three decades, the integrase (Int) from Streptomyces phage phiC31 has become a valuable genome engineering tool across various species. phiC31 Int was thought to mediate unidirectional site-specific integration (attP × attB to attL and attR) in the absence of the phage-encoded recombination directionality factor (RDF). However, we have shown in this study that Int can also catalyze reverse excision (attL × attR to attP and attB) at low frequencies in Streptomyces lividans and Escherichia coli, causing genetic instability in engineered strains. To address this issue, we developed a two-plasmid co-conjugation (TPC) system. This system consists of an attP-containing integration vector and an Int expression suicide plasmid, both carrying oriT to facilitate efficient conjugation transfer from E. coli to Streptomyces. Using the TPC system, genetically stable integrants free of Int can be generated quickly and easily. The indigoidine-producing strains generated by the TPC system exhibited higher genetic stability and production efficiency compared to the indigoidine-producing strain generated by the conventional integration system, further demonstrating the utility of the TPC system in the field of biotechnology. We anticipate that the strategies presented here will be widely adopted for stable genetic engineering of industrial microbes using phage integrase-based integration systems.IMPORTANCELarge serine recombinases (LSRs), including the bacteriophage phiC31 integrase, were previously thought to allow only unidirectional site-specific integration (attP × attB to attL and attR). Our study is the first to show that the phiC31 integrase can also catalyze a low-efficiency reverse excision reaction in Streptomyces and E. coli without the involvement of the phage-encoded recombination directionality factor (RDF). The genetic instability caused by the low in vivo excisionase activity of the phiC31 integrase is a major challenge for biotechnological applications. Our study addresses this issue by developing a two-plasmid co-conjugation (TPC) system that facilitates the construction of Int-deficient genomic engineering strains. The Int-deficient integrants produced by this TPC system exhibit strong genetic stability for introduced genes and maintain stable production traits even in the absence of selection pressure, making them highly valuable for industrial applications.

Biogenic synthesis of titanium nanoparticles by Streptomyces rubrolavendulae for sustainable management of Icerya aegyptiaca (Douglas)

Biosynthesized nanoparticles have a variety of applications, and microorganisms are considered one of the most ideal sources for the synthesis of green nanoparticles. Icerya aegyptiaca (Douglas) is a pest that has many generations per year and can affect 123 plant species from 49 families by absorbing sap from bark, forming honeydew, causing sooty mold, and attracting invasive ant species, leading to significant agricultural losses. The purpose of this work was to synthesize titanium dioxide nanoparticles (TiO2-NPs) from marine actinobacteria and evaluate their insecticidal effects on Icerya aegyptiaca (Hemiptera: Monophlebidae), in addition to explaining their effects on protein electrophoresis analysis of SDS‒PAGE proteins from control and treated insects after 24, 72 and 120 h of exposure. In all, seven actinobacterial isolates, the most potent of which has the potential to produce titanium hydroxide-based nanoparticles (TiO2-NP2), have DNA sequences that are 99.9% like those of Streptomyces rubrolavendulae (MCN2) according to nucleotide alignment and a phylogenetic tree. The produced TiO2-NPs were verified by UV examination and characterized by FT-IR, XRD, TEM, EDX, and DLS analyses. Toxicological results revealed that TiO2-NPs have insecticidal effects and high mortality rates reaching 55, 62.5, 80 and 95% at TiO2-NPs dose 120,250,500 and 1000 ppm respectively. Compared with the control, TiO2-NP spraying caused changes in the protein pattern of I. aegyptiaca, as indicated by the disappearance of normal bands and the appearance of other bands, as well as quantitative and qualitative changes in protein content after 24, 72 and 120 h of exposure. The application of TiO2-NPs by MNC2 offers a new alternative strategy to control I. aegyptiaca and is considered a modern approach to nanotechnology.

StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization

Streptomycetes remain an important bacterial source of natural products (NPs) with significant therapeutic promise, particularly in the fight against antimicrobial resistance. Herein, we present StreptomeDB 4.0, a substantial update of the database that includes expanded content and several new features. Currently, StreptomeDB 4.0 contains over 8500 NPs originating from ∼3900 streptomycetes, manually annotated from ∼7600 PubMed-indexed peer-reviewed articles. The database was enhanced by two in-house developments: (i) automated literature-mined NP-protein relationships (hyperlinked to the CPRiL web server) and (ii) pharmacophore-based NP-protein interactions (predicted with the ePharmaLib dataset). Moreover, genome mining was supplemented through hyperlinks to the widely used antiSMASH database. To facilitate NP structural dereplication, interactive visualization tools were implemented, namely the JSpecView applet and plotly.js charting library for predicted nuclear magnetic resonance and mass spectrometry spectral data, respectively. Furthermore, both the backend database and the frontend web interface were redesigned, and several software packages, including PostgreSQL and Django, were updated to the latest versions. Overall, this comprehensive database serves as a vital resource for researchers seeking to delve into the metabolic intricacies of streptomycetes and discover novel therapeutics, notably antimicrobial agents. StreptomeDB is publicly accessible at https://www.pharmbioinf.uni-freiburg.de/streptomedb.

Isolation of Actinobacteria from Date Palm Rhizosphere with Enzymatic, Antimicrobial, Antioxidant, and Protein Denaturation Inhibitory Activities

Arid ecosystems constitute a promising source of actinobacteria producing new bioactive molecules. This study aimed to explore different biological activities of actinomycetes isolated from the rhizosphere of Phoenix dactylifera L. in the Ghardaia region, Algeria. A total of 18 actinobacteria were isolated and studied for their enzymatic and antimicrobial activities. All isolates shared cellulase and catalase activity; most of them produced amylase (94%), esterase (84%), lecithinase and lipoproteins (78%), caseinase (94%), and gelatinase (72%). The isolates could coagulate (56%) or peptonize (28%) skim milk. Overall, 72% of the isolates exhibited significant antibacterial activity against at least one test bacteria, while 56% demonstrated antifungal activity against at least one test fungi. Based on enzyme production and antimicrobial activity, isolate SGI16 was selected for secondary metabolite extraction by ethyl acetate. The crude extract of SGI16 was analyzed using DPPH and BSA denaturation inhibition tests, revealing significant antioxidant power (IC50 = 7.24 ± 0.21 μg mL-1) and protein denaturation inhibitory capacity (IC50 = 492.41 ± 0.47 μg mL-1). Molecular identification based on 16S rDNA analysis showed that SGI16 belonged to the genus Streptomyces. The findings highlight that date palms' rhizosphere actinobacteria are a valuable source of biomolecules of biotechnological interest.

Current Approaches for Genetic Manipulation of Streptomyces spp.-Key Bacteria for Biotechnology and Environment

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, medical and agricultural use. Although Streptomyces spp. have been studied for decades, the engineering of these bacteria remains challenging, and the available genetic tools are rather limited. Furthermore, most biosynthetic gene clusters in these bacteria are silent and require strategies to activate them and exploit their production potential. In order to explore, understand and manipulate the capabilities of Streptomyces spp. as a key bacterial for biotechnology, synthetic biology strategies emerged as a valuable component of Streptomyces research. Recent advancements in strategies for genetic manipulation of Streptomyces involving proposals of a large variety of synthetic components for the genetic toolbox, as well as new approaches for genome mining, assembly of genetic constructs and their delivery into the cell, allowed facilitation of the turnaround time of strain engineering and efficient production of new natural products at an industrial scale, but still have strain- and design-dependent limitations. A new perspective offered recently by technical advances in DNA sequencing, analysis and editing proposed strategies to overcome strain- and construct-specific difficulties in the engineering of Streptomyces. In this review, challenges and recent developments of approaches for Streptomyces engineering are discussed, an overview of novel synthetic biology strategies is provided and examples of successful application of new technologies in molecular genetic engineering of Streptomyces are highlighted.

Biocontrol potential of Streptomyces sp. N2 against green and blue mold disease in postharvest navel orange and the action mechanism

The objective of this study was to provide a promising alternative to chemical fungicides for management of postharvest citrus decay, thereby promoting sustainable citrus fruit production. The postharvest decay of citrus fruit caused by Penicillium digitatum and Penicillium italicum results in substantial economic losses in citrus industry worldwide. With growing fungal resistance issues in P. digitatum and P. italicum, there is an urgent need for searching new methods to address above problems in a safe and environmentally friendly way. Streptomyces sp. N2, a new species from Streptomyces genus, exhibits significant antagonistic activity against Rhizoctonia solani. However, its biocontrol efficacy against postharvest decay caused by P. digitatum and P. italicum and its action mechanism remain unknown. In this study, Streptomyces sp. N2 was found to have significant potential in controlling green and blue mold diseases in postharvest navel oranges. Moreover, the action mechanism of Streptomyces sp. N2 against both P. italicum and P. digitatum was elucidated. On the one hand, Streptomyces sp. N2 stimulated fruit resistance to fight against invading fungal pathogens. It significantly reduced ROS content in navel orange upon the infection of mold disease, increased the production of defense-related enzymes including peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) and pathogenesis-related proteins of chitinase and β-1,3-glucanase. On the other hand, Streptomyces sp. N2 secreted bioactive substances to inhibit the growth of P. italicum and P. digitatum so as to prevent the development of postharvest decay. The bioactive substances secreted by Streptomyces sp. N2 significantly inhibited the spore germination and mycelial growth and led to microstructural damages to the cell wall and membrane, ROS burst, and mitochondrial dysfunction in both P. italicum and P. digitatum. This study provides a theoretical reference and application potential for the biological control of Streptomyces sp. N2 on green and blue mold diseases.

The faucet knob effect of DptE crotonylation on the initial flow of daptomycin biosynthesis

We propose here that acylation modification of actinomycete proteins is a restrictive system that limits the excessive synthesis of secondary metabolites, its mechanism has not been clearly elucidated before. We used crotonylation as an example to investigate the acylation effect in the daptomycin biosynthesis by Streptomyces roseosporus. Our experiments revealed abundant crotonylation of numerous secondary metabolic enzymes in Streptomyces roseosporus, a daptomycin producer. DptE, which initiates daptomycin biosynthesis, is crotonylated at K454. We experimentally identified the corresponding DptE crotonyltransferase Kct1 and decrotonylase CobB. Further studies consistently confirmed that decrotonylation increases DptE activity. Decrotonylation functions like loosening a faucet knob, increasing substrate channel throughput and the initial flow of daptomycin biosynthesis. Moreover, DptE catalytic activity was enhanced via K454 and neighboring residues K184 and Q420 mutation, increasing daptomycin yield by 132%; daptomycin biosynthesis related metabolism activities also increased. Substrate channel prediction revealed 38% higher throughput for mutant DptE (K454I/K184Q/Q420N) than crotonylated DptE. Molecular dynamics (MD) simulations revealed significant increases in flexibility and substrate affinity of the mutant. In summary, we elucidated the faucet knob effect of DptE crotonylation on the initial flow of daptomycin biosynthesis and adopted decrotonylation to generate high-yield industrial strains.

Biocontrol of Mycotoxigenic Fungi by Actinobacteria

Actinobacteria are well known for their production of metabolites of interest. They have been previously studied to identify new antibiotics in medical research and for their ability to stimulate plant growth in agronomic research. Actinobacteria represents a real source of potential biocontrol agents (BCAs) today. With the aim of reducing the use of phytosanitary products by 50% with the different Ecophyto plans, a possible application is the fight against mycotoxin-producing fungi in food matrices and crops using BCAs. To deal with this problem, the use of actinobacteria, notably belonging to the Streptomyces genus, or their specialized metabolites seems to be a solution. In this review, we focused on the impact of actinobacteria or their metabolites on the development of mycotoxigenic fungi and mycotoxin production on the one hand, and on the other hand on their ability to detoxify food matrices contaminated by mycotoxins.

Genomic and Phenotypic Characterization of Streptomyces sirii sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil

In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of Bambusa vulgaris. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA-DNA hybridization calculation indicated that BP-8 represents the type strain of a novel Streptomyces species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of Streptomyces. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8T (=VKM Ac-3066T = CCTCC AA 2024094T) is proposed as the type strain of the novel species Streptomyces sirii sp. nov.

Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove

A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.

Streptomyces albidocamelliae sp. nov., an endophytic actinomycete isolated from the leaves of Camellia oleifera

A novel actinobacterium strain, HUAS 14-6T, was isolated from the healthy leaves of Camellia oleifera collected from Changde City, Hunan Province, China. Strain HUAS 14-6T produced tight spiral spore chains consisting of oval or spherical spores with a smooth surface. 16S rRNA gene sequence analysis revealed that strain HUAS 14-6T belonged to the genus Streptomyces and shared highest similarity to Streptomyces bungoensis DSM 41781T (99.72%). Phylogenetic analysis based on 16S rRNA gene sequences indicated strain HUAS 14-6T was in a clade with S. bungoensis DSM 41781T. However, the ANIm and dDDH between strain HUAS 14-6T and S. bungoensis DSM 41781T were 88.16% and 31.2%, respectively, far less than the species-level thresholds. Phylogenetic trees based on the five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that strain HUAS 14-6T formed a separate branch, indicating that this strain could belong to a potential new species. Pairwise MLSA distances between strain HUAS 14-6T and all type strains exhibiting 16S rRNA gene sequence similarities of ≥98.7% to it were much higher than the maximum range of 0.014 recommended for delineating a new Streptomyces species. Based on polyphasic taxonomic study, HUAS 14-6T represents a novel species within the genus Streptomyces for which the name Streptomyces albidocamelliae sp. nov. is proposed. The type strain is HUAS 14-6T (=MCCC 1K08365T=JCM 35920T).

Functional analysis of the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439

Cytochrome P450 enzymes (CYPs or P450s) and ferredoxins (Fdxs) are ubiquitously distributed in all domains of life. Bacterial P450s are capable of catalyzing various oxidative reactions with two electrons usually donated by Fdxs. Particularly in Streptomyces, there are abundant P450s that have exhibited outstanding biosynthetic capacity of bioactive metabolites and great potential for xenobiotic metabolisms. However, no systematic study has been conducted on physiological functions of the whole cytochrome P450 complement (CYPome) and ferredoxin complement (Fdxome) of any Streptomyces strain to date, leaving a significant knowledge gap in microbial functional genomics. Herein, we functionally analyze the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439 by investigating groups of single and sequential P450 deletion mutants, single P450 overexpression mutants, and Fdx gene deletion or repression mutants. Construction of an unprecedented P450-null mutant strain indicates that none of P450 genes are essential for S. venezuelae in maintaining its survival and normal morphology. The non-housekeeping Fdx1 and housekeeping Fdx3 not only jointly support the cellular activity of the prototypic P450 enzyme PikC, but also play significant regulatory functions. These findings significantly advance the understandings of the native functionality of P450s and Fdxs as well as their cellular interactions.