Refining the Natural Product Repertoire in Entomopathogenic Bacteria

Unveiling the Bioactive Potential of Bacterial Isolates from Extreme Environments of Pakistan by In Vitro and In Silico Approaches

The soil hosts a wide array of bacterial species capable of producing diverse bioactive compounds. This research aimed to screen bacterial isolates for their bioactive potential from extreme environments in Pakistan. Out of the 69 isolates examined, only 7 exhibited antagonistic activity against Bacillus sp. and Escherichia coli test strains. Notably, the B. cereus DS-2 strain demonstrated the highest antibacterial potential (31 mm and 15 mm) against the Bacillus and E. coli test strains, respectively. Mode-of-action studies suggested that the crude extract might have induced morphological abnormalities in the Bacillus sp. (test strain), causing cell contraction, chain breakage, and deformation. Furthermore, the B. cereus DS-2 strain displayed significant antioxidant potential (64.8%) as revealed by the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. Thin-layer chromatography (TLC) of the DS-2 crude extract led to the separation of six components, with only spots 3 and 4 exhibiting the antibacterial potential (3 mm and 5 mm, respectively). Subsequently, gas chromatography-mass spectrometry (GC-MS) analysis of the bioactive fraction extracted from TLC revealed the presence of diisooctyl phthalate, dibutyl phthalate, hexadecanoic acid methyl ester, and octadecanoic acid methyl ester. Molecular docking analysis of diisooctyl phthalate and dibutyl phthalate revealed their binding affinity against E. coli and Bacillus sp. targets. ADMET analysis confirmed the solubility, toxicity, and drug-like properties of the ligands based on Lipinski's rule of five. Current findings suggest that these compounds hold promise as antibacterial agents in drug development. This study underscores the diverse microbial community present in extreme environments and highlights the versatile applications of natural products derived from these strains.

Small molecule produced by Photorhabdus interferes with ubiquinone biosynthesis in Gram-negative bacteria

We report the identification of 3,6-dihydroxy-1,2-benzisoxazole (DHB) in a screen of Photorhabdus and Xenorhabdus, whose symbiotic relationship with eukaryotic nematodes favors secondary metabolites that meet several requirements matching those for clinically useful antibiotics. DHB is produced by Photorhabdus laumondii and is selective against the Gram-negative species Escherichia coli, Enterobacter cloacae, Serratia marcescens, Klebsiella pneumoniae, Proteus mirabilis, and Acinetobacter baumannii. It is inactive against anaerobic gut bacteria and nontoxic to human cells. Mutants resistant to DHB map to the ubiquinone biosynthesis pathway. DHB binds to 4-hydroxybenzoate octaprenyltransferase (UbiA) and prevents the formation of 4-hydroxy-3-octaprenylbenzoate. Remarkably, DHB itself is prenylated, forming an unusable chimeric product that likely contributes to the toxic effect of this antimicrobial. DHB appears to be both a competitive enzyme inhibitor and a prodrug; this dual mode of action is unusual for an antimicrobial compound.

IMPORTANCE

The spread of resistant pathogens has led to the antimicrobial resistance crisis, and the need for new compounds acting against Gram-negative pathogens is especially acute. From a screen of Photorhabdus symbionts of nematodes, we identified 3,6-dihydroxy-1,2-benzisoxazole (DHB) that acts against a range of Gram-negative bacteria, including Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, and Acinetobacter baumannii. DHB had previously been isolated from other bacterial species, but its mechanism of action remained unknown. We show that DHB is unique among antimicrobials, with dual action as an inhibitor of an important enzyme, UbiA, in the biosynthesis pathway of ubiquinone and as a prodrug. DHB is a mimic of the natural substrate, and UbiA modifies it into a toxic product, contributing to the antimicrobial action of this unusual antibiotic. We also uncover the mechanism of DHB selectivity, which depends on a particular fold of the UbiA enzyme.

Natural products from Xenorhabdus and Photorhabdus show promise as biolarvicides against Aedes albopictus

BACKGROUND

In the perpetual struggle to manage mosquito populations, there has been increasing demand for the development of biopesticides to supplant/complement current products. The insecticidal potential of Xenorhabdus and Photorhabdus has long been recognized and is of interest for the control of important mosquitoes like Aedes albopictus which vectors over 20 different arboviruses of global public health concern.

RESULTS

The larvicidal effects of cell-free supernatants, cell growth cultures and cell mass of an extensive list of Xenorhabdus and Photorhabdus spp. was investigated. They were quite effective against Ae. albopictus causing larval mortality ranging between 52-100%. Three Photorhabdus spp. and 13 Xenorhabdus spp. release larvicidal compounds in cell-free supernatants. Cell growth culture of all tested species exhibited larvicidal activity, except for Xenorhabdus sp. TS4. Twenty-one Xenorhabdus and Photorhabdus bacterial cells (pellet) exhibited oral toxicity (59-91%) against exposed larvae. The effect of bacterial supernatants on the mosquito eggs were also assessed. Bacterial supernatants inhibited the hatching of mosquito eggs; when unhatched eggs were transferred to clean water, they all hatched. Using the easyPACId approach, the larvicidal compounds in bacterial supernatant were identified as fabclavine from X. szentirmaii and xencoumacin from X. nematophila (causing 98 and 70% mortality, respectively, after 48 h). Xenorhabdus cabanillasii and X. hominickii fabclavines were as effective as commercial Bacillus thuringiensis subsp. israelensis and spinosad products within 5 days post-application (dpa).

CONCLUSION

Fabclavine and xenocoumacin can be developed into novel biolarvicides, can be used as a model to synthesize other compounds or/and can be combined with other commercial biolarvicides. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.

The insect microbiome is a vast source of bioactive small molecules

Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.

Ligands of HMG-like dorsal switch protein 1 of Spodoptera exigua leads to mortality in diamondback moth, Plutellaxylostella

HMG-like dorsal switch protein 1 (DSP1) is the insect homolog of the high mobility group box 1 (HMGB1) protein of the vertebrates. Previous studies confirmed DSP1 in Spodoptera exigua, Tenebrio molitor, and Aedes albopictus, and were analyzed for their immune roles, survivability, and binding affinity with entomopathogenic bacterial metabolites. The present study aimed to predict, and confirm DSP1 in diamondback moth, Plutella xylostella along with the effect of Spodoptera exigua DSP1 ligands in the survivability of this insect. DSP1 of Plutella xylostella (Px-DSP1) consists of 465 amino acids (AA). Phylogeny analysis showed that Px-DSP1 clustered with other Lepidopteran insects where each insect order clustered separately. Domain analysis showed that like other insects, Px-DSP1 contains two HMG boxes (Box A and Box B), one coiled-coil (CC), five Q-rich low complexity (LC), and an acidic tail (AT). Px-DSP1 was expressed in each developmental stage and tissue. The highest expression was in L4 larvae and fat body tissues. Thermal shift assay (TSA) showed the binding affinity of 3-Ethoxy-4-Methoxyphenol (EMP), Phthalimide (PM), and o-Cyanobenzoic acid (CBA) to rDSP1 of Spodoptera exigua. Mortality bioassay showed that all these metabolites were toxic against P. xylostella larvae. Among these, EMP was more toxic providing more than 65% mortality at 500 ppm concentration. However, PM and CBA also showed more than 60 and 50% mortality, respectively at 500 ppm concentration. We assume that like Se-DSP1, these compounds also bind with Px-DSP1 which leads to the inhibition of DSP1-mediated immunity and impose the mortality of Plutella xylostella larvae.

Biosynthesis of selenium nanoparticles using cell-free extract of Xenorhabdus cabanillasii GU480990 and their potential mosquito larvicidal properties against yellow fever mosquito Aedes aegypti

Nanomaterials are successful due to their numerous applications in various domains such as cancer treatment, environmental applications, drug and gene delivery. Selenium is a metalloid element with broad biological activities and low toxicity especially at the nanoscale. Several studies have shown that nanoparticles synthesized from microbial and plant extracts are effective against important pests and pathogens. This study describes the bio fabrication of selenium nanoparticles using cell free extract of Xenorhabdus cabanillasii (XC-SeNPs) and assessed their mosquito larvicidal properties. Crystallographic structure and size of XC-SeNPs were determined with UV-a spectrophotometer, Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction analysis (XRD), Energy-dispersive X-ray spectroscopy (EDAX), Zeta potential and Transmission electron microscopy (TEM). The significant surface plasmon resonance at 275 nm indicated the synthesis of XC-SeNPs from the pure cell-free extract of X. cabanillasii. The XRD result exhibits the crystalline nature of XC-SeNPs. The Zeta potential analysis confirmed that the surface charge of XC-SeNPs was -24.17 mV. TEM analysis revealed that synthesized XC-SeNPs were monodispersed, spherically shaped, and sized about 80-200 nm range. In addition, the larvicidal potentials of the bio-fabricated XC-SeNPs were assessed against the 4th-instar Ae. aegypti. XC-SeNPs displayed a dose-dependent larvicidal effect; the larval mortality was 13.3 % at the minimum evaluated concentration and increased to 72 % at higher dose treatments. The LC50 and LC90 concentration of XC-SeNPs against mosquito larvae were 79.4 and 722.4 ppm, respectively.

Discovery of an antitumor compound from xenorhabdus stockiae HN_xs01

Xenorhabdus, known for its symbiotic relationship with Entomopathogenic nematodes (EPNs), belongs to the Enterobacteriaceae family. This dual-host symbiotic nematode exhibits pathogenic traits, rendering it a promising biocontrol agent against insects. Our prior investigations revealed that Xenorhabdus stockiae HN_xs01, isolated in our laboratory, demonstrates exceptional potential in halting bacterial growth and displaying anti-tumor activity. Subsequently, we separated and purified the supernatant of the HN_xs01 strain and obtained a new compound with significant inhibitory activity on tumor cells, which we named XNAE. Through LC-MS analysis, the mass-to-nucleus ratio of XNAE was determined to be 254.24. Our findings indicated that XNAE exerts a time- and dose-dependent inhibition on B16 and HeLa cells. After 24 h, its IC50 for B16 and HeLa cells was 30.178 µg/mL and 33.015 µg/mL, respectively. Electron microscopy revealed conspicuous damage to subcellular structures, notably mitochondria and the cytoskeleton, resulting in a notable reduction in cell numbers among treated tumor cells. Interestingly, while XNAE exerted a more pronounced inhibitory effect on B16 cells compared to HeLa cells, it showed no discernible impact on HUVEC cells. Treatment of B16 cells with XNAE induced early apoptosis and led to cell cycle arrest in the G2 phase, as evidenced by flow cytometry analysis. The impressive capability of X. stockiae HN_xs01 in synthesizing bioactive secondary metabolites promises to significantly expand the reservoir of natural products. Further exploration to identify the bioactivity of these compounds holds the potential to shed light on their roles in bacteria-host interaction. Overall, these outcomes underscore the promising potential of XNAE as a bioactive compound for tumor treatment.

The Lrp transcriptional factor of an entomopathogenic bacterium, Xenorhabdus hominickii, activates non-ribosomal peptide synthetases to suppress insect immunity

Two bacterial genera, Xenorhabdus and Photorhabdus, are mutually symbiotic to the entomopathogenic nematodes, Steinernema and Heterorhabditis, respectively. The infective juveniles deliver the symbiotic bacteria to the hemocoel of target insects, in which the bacteria proliferate and help the development of the host nematode. The successful parasitism of the nematode-bacterial complex depends on host immunosuppression by the bacteria via their secondary metabolites. Leucine-responsive regulatory protein (Lrp) is a global bacterial transcriptional factor that plays a crucial role in parasitism. However, its regulatory targets to suppress insect immunity are not clearly understood. This study investigated the bacterial genes regulated by Lrp and the subsequent production of secondary metabolites in Xenorhabdus hominickii. Lrp expression occurred at the early infection stage of the bacteria in a target insect, Spodoptera exigua. A preliminary in silico screening indicated that 3.7% genes among 4075 predicted genes encoded in X. hominickii had the Lrp-response element on their promoters, including two non-ribosomal peptide synthetases (NRPSs). Eight NRPS (NRPS1-NRPS8) genes were predicted in the bacterial genome, in which six NRPS (NRPS3-NRPS8) expressions were positively correlated with Lrp expression in the infected larvae of S. exigua. Exchange of the Lrp promoter with an inducible promoter altered the production of the secondary metabolites and the NRPS expression levels. The immunosuppressive activities of X. hominickii were dependent on the Lrp expression level. The metabolites produced by Lrp expression included the eicosanoid-biosynthesis inhibitors and hemolytic factors. A cyclic dipeptide (=cPF) was produced by the bacteria at high Lrp expression and inhibited the phospholipase A2 activity of S. exigua in a competitive inhibitory manner. These results suggest that Lrp is a global transcriptional factor of X. hominickii and plays a crucial role in insect immunosuppression by modulating NRPS expression.

Identification of fabclavine derivatives, Fcl-7 and Fcl-8, from Xenorhabdus budapestensis as major antifungal natural products against Rhizoctonia solani

AIMS

Black scurf disease, caused by Rhizoctonia solani, is a severe soil-borne and tuber-borne disease, which occurs and spreads in potato growing areas worldwide and poses a serious threat to potato production. New biofungicide is highly desirable for addressing the issue, and natural products (NPs) from Xenorhabdus spp. provide prolific resources for biofungicide development. In this study, we aim to identify antifungal NPs from Xenorhabdus spp. for the management of this disease.

METHODS AND RESULTS

Out of the 22 Xenorhabdus strains investigated, Xenorhabdus budapestensis 8 (XBD8) was determined to be the most promising candidate with the measured IC50 value of its cell-free supernatant against R. solani as low as 0.19 ml l-1. The major antifungal compound in XBD8 started to be synthesized in the middle logarithmic phase and reached a stable level at stationary phase. Core gene deletion coupled with high-resolution mass spectrometry analysis determined the major antifungal NPs as fabclavine derivatives, Fcl-7 and 8, which showed broad-spectrum bioactivity against important pathogenic fungi. Impressively, the identified fabclavine derivatives effectively controlled black scurf disease in both greenhouse and field experiments, significantly improving tuber quality and increasing with marketable tuber yield from 29 300 to 35 494 kg ha-1, comparable with chemical fungicide fludioxonil.

CONCLUSIONS

The fabclavine derivatives Fcl-7 and 8 were determined as the major antifungal NPs in XBD8, which demonstrated a bright prospect for the management of black scurf disease.

Persephacin Is a Broad-Spectrum Antifungal Aureobasidin Metabolite That Overcomes Intrinsic Resistance in Aspergillus fumigatus

Fungi pose a persistent threat to humankind with worrying indications that emerging and re-emerging pathogens (e.g., Candida auris, Coccidioides spp., drug-resistant Aspergilli, and more) exhibit resistance to the limited number of approved antifungals. To address this problem, our team is exploring endophytic fungi as a resource for the discovery of new antifungal natural products. The rationale behind this decision is based on evidence that endophytes engage with plants in mutualistic relationships wherein some fungi actively participate by producing chemical defense measures that suppress pathogenic microorganisms. To improve the odds of bioactive metabolite discovery, we developed a new hands-free laser-cutting system capable of generating >50 plant samples per minute that, in turn, enabled our team to prepare and screen large numbers of endophytic fungi. One of the fungal isolates obtained in this way was identified as an Elsinoë sp. that produced a unique aureobasidin analogue, persephacin (1). Some distinctive features of 1 are the absence of both phenylalanine residues combined with the incorporation of a novel amino acid residue, persephanine (9). Compound 1 exhibits potent antifungal effects against a large number of pathogenic yeast (including several clinical C. auris strains), as well as phylogenetically diverse filamentous fungi (e.g., Aspergillus fumigatus). In an ex vivo eye infection model, compound 1 outperformed standard-of-care treatments demonstrating the ability to suppress fluconazole-resistant Candida albicans and A. fumigatus at a concentration (0.1% solution) well below the clinically recommended levels used for fluconazole and natamycin (2% and 5% solutions, respectively). In 3D tissue models for acute dermal and ocular safety, 1 was found to be nontoxic and nonirritating at concentrations required to elicit antifungal activity. Natural product 1 appears to be a promising candidate for further investigation as a broad-spectrum antifungal capable of controlling a range of pathogens that negatively impact human, animal, and plant health.

Photorhabdus aballayi sp. nov. and Photorhabdus luminescens subsp. venezuelensis subsp. nov., isolated from Heterorhabditis amazonensis entomopathogenic nematodes

Six Gram-negative, rod-shaped bacterial strains isolated from Heterorhabditis amazonensis entomopathogenic nematodes were characterized to determine their taxonomic position. 16S rRNA and gyrB gene sequences indicate that they belong to the class Gammaproteobacteria, family Morganellaceae and genus Photorhabdus, and that some of them are conspecifics. Two of them, APURE^T and JAR^T, were selected for further molecular characterization using whole genome- and whole-proteome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions using whole genome and whole proteome sequences show that strains APURE^T and JAR^T are closely related to Photorhabdus luminescens subsp. luminescens ATCC 29999^T and to P. luminescens subsp. mexicana MEX47-22^T. Moreover, digital DNA-DNA hybridization (dDDH) values between APURE^T and P. luminescens subsp. luminescens ATCC 29999^T, APURE^T and P. luminescens subsp. mexicana MEX47-22^T, and APURE^T and JAR^T are 61.6, 61.2 and 64.1 %, respectively. These values are below the 70 % divergence threshold that delimits prokaryotic species. dDDH scores between JAR^T and P. luminescens subsp. luminescens ATCC 29999^T and between JAR^T and P. luminescens subsp. mexicana MEX47-22^T are 71.9 and 74.8 %, respectively. These values are within the 70 and 79 % divergence thresholds that delimit prokaryotic subspecies. Based on these genomic divergence values, APURE^T and JAR^T represent two different taxa, for which we propose the names: Photorhabdus aballayi sp. nov. with APURE^T (=CCM 9236^T =CCOS 2019^T) as type strain and Photorhabdus luminescens subsp. venezuelensis subsp. nov. with JAR^T (=CCM 9235^T =CCOS 2021^T) as type strain. Our study contributes to a better understanding of the biodiversity of an important bacterial group with enormous biotechnological and agricultural potential.

Identification of Fcl-29 as an Effective Antifungal Natural Product against Fusarium graminearum and Combinatorial Engineering Strategy for Improving Its Yield

Fusarium head blight (FHB), caused by Fusarium graminearum, whose occurrence and prevalence causes 10-70% wheat production loss, is one of the most destructive diseases influencing the production of wheat globally. To identify the potential natural products (NPs) against F. graminearum, we screened 59 Xenorhabdus strains and discovered that the cell-free supernatant (CFS) of X. budapestensis 14 (XBD14) displays the highest bioactivity. Multiple genetic methods coupled with HRMS/MS analysis determined the major antifungal NP to be Fcl-29, a fabclavine derivative. Fcl-29 was found to effectively control FHB of wheat in the field test and demonstrated broad-spectrum antifungal activity against important pathogenic fungi. The production of Fcl-29 was dramatically improved by 33.82-fold with the combinatorial strategy of genetic engineering (1.66-fold) and fermentation engineering (20.39-fold). The exploration of a new biofungicide in global plant protection is now possible.

Evaluation of Entomopathogenic Nematodes against Common Wireworm Species in Potato Cultivation

Wireworms (Coleoptera: Elateridae) are common insect pests that attack a wide range of economically important crops including potatoes. The control of wireworms is of prime importance in potato production due to the potential damage of the larvae to tuber quantity and quality. Chemical insecticides, the main control strategy against wireworms, generally fail to provide satisfactory control due to the lack of available chemicals and the soil-dwelling habits of the larvae. In the last decades, new eco-friendly concepts have emerged in the sustainable control of wireworms, one of which is entomopathogenic nematodes (EPNs). EPNs are soil-inhabitant organisms and represent an ecological approach to controlling a great variety of soil-dwelling insect pests. In this study, the susceptibility of Agriotes sputator Linnaeus and A. rufipalpis Brullé larvae, the most common wireworm species in potato cultivation in Türkiye, to native EPN strains [Steinernema carpocapsae (Sc_BL22), S. feltiae (Sf_BL24 and Sf_KAY4), and Heterorhabditis bacteriophora (Hb_KAY10 and Hb_AF12)] were evaluated at two temperatures (25 and 30 °C) in pot experiments. Heterorhabditis bacteriophora Hb_AF12 was the most effective strain at 30 °C six days post-inoculation and caused 37.5% mortality to A. rufipalpis larvae. Agriotes sputator larvae were more susceptible to tested EPNs at the same exposure time, and 50% mortality was achieved by two EPNs species, Hb_AF12 and Sc_BL22. All EPN species/strains induced mortality over 70% to both wireworm species at both temperatures at 100 IJs/cm², 18 days post-treatment. The results suggest that tested EPN species/strains have great potential in the control of A. sputator and A. rufipalpis larvae.

Non-ribosomal peptide biosynthetic potential of the nematode symbiont Photorhabdus

Photorhabdus, the symbiotic bacteria of Heterorhabditis nematodes, has been reported to possess many non-ribosomal peptide synthetase (NRPS) biosynthesis gene clusters (BGCs). To provide an in-depth assessment of the non-ribosomal peptide biosynthetic potential of Photorhabdus, we compared the distribution of BGCs in 81 Photorhabdus strains, confirming the predominant presence (44.80%) of NRPS BGCs in Photorhabdus. All 990 NRPS BGCs were clustered into 275 gene cluster families (GCFs) and only 13 GCFs could be annotated with known BGCs, suggesting their great diversity and novelty. These NRPS BGCs encoded 351 novel peptides containing more than four amino acids, and 173 of them showed high sequence similarity to known BGCs encoding bioactive peptides, implying the promising potential of Photorhabdus to produce valuable peptides. Sequence similarity networking of adenylation (A-) domains suggested that the substrate specificity of A-domains was not directly correlated with the sequence similarity. The molecular similarity network of predicted metabolite scaffolds of NRPS BGCs and reported peptides from Photorhabdus and a relevant database demonstrated that the non-ribosomal peptide biosynthetic potential of Photorhabdus was largely untapped and revealed the core peptides deserving intensive studies. Our present study provides valuable information for the targeted discovery of novel non-ribosomal peptides from Photorhabdus.

Computational identification of a systemic antibiotic for gram-negative bacteria

Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA. We reasoned that a computational search for genes only distantly related to the darobactin operon may lead to novel compounds. Following this clue, we identified dynobactin A, a novel peptide antibiotic from Photorhabdus australis containing two unlinked rings. Dynobactin is structurally unrelated to darobactins, but also targets BamA. Based on a BamA-dynobactin co-crystal structure and a BAM-complex-dynobactin cryo-EM structure, we show that dynobactin binds to the BamA lateral gate, uniquely protruding into its β-barrel lumen. Dynobactin showed efficacy in a mouse systemic Escherichia coli infection. This study demonstrates the utility of computational approaches to antibiotic discovery and suggests that dynobactin is a promising lead for drug development.

Integrated Biological Control Using a Mixture of Two Entomopathogenic Bacteria, Bacillus thuringiensis and Xenorhabdus hominickii, against Spodoptera exigua and Other Congeners

Insect immunity defends against the virulence of various entomopathogens, including Bacillus thuringiensis (Bt). This study tested a hypothesis that any suppression of immune responses enhances Bt virulence. In a previous study, the entomopathogenic bacterium, Xenorhabdus hominickii (Xh), was shown to produce secondary metabolites to suppress insect immune responses. Indeed, the addition of Xh culture broth (XhE) significantly enhanced the insecticidal activity of Bt against S. exigua. To analyze the virulence enhanced by the addition of Xh metabolites, four bacterial secondary metabolites were individually added to the Bt treatment. Each metabolite significantly enhanced the Bt insecticidal activity, along with significant suppression of the induced immune responses. A bacterial mixture was prepared by adding freeze-dried XhE to Bt spores, and the optimal mixture ratio to kill the insects was determined. The formulated bacterial mixture was applied to S. exigua larvae infesting Welsh onions in a greenhouse and showed enhanced control efficacy compared to Bt alone. The bacterial mixture was also effective in controlling other Spodopteran species such as S. litura and S. frugiperda but not other insect genera or orders. This suggests that Bt+XhE can effectively control Spodoptera-associated pests by suppressing the immune defenses.

A novel tumor-targeting strain of Xenorhabdus stockiae exhibits potent biological activities

Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema presenting two distinct forms in their life cycle, and can produce a broad range of bioactive compounds. In this study, a novel Xenorhabdus stockiae strain HN_xs01 was isolated from a soil sample via an entrapment method using Galleria melonella nematodes. The supernatants of strain HN_xs01 exhibited antimicrobial properties against Gram-negative and Gram-positive bacteria, and insecticidal properties against Helicoverpa armigera larvae, and antitumor properties as well. Moreover, three linear rhabdopeptides (1, 2 and 3) were identified from strain HN_xs01 using nuclear magnetic resonance analysis, which exhibited significant cytotoxic activity against the human epithelial carcinoma cell line A431 and the human chronic myelogenous leukemia cell line K562. Some bacteria have been reported to colonize the tumor region, and we determined that HN_xs01 could grow in tumor xenografts in this study. HN_xs01 invaded and replicated in B16 melanoma cells grafted into C57BL/6 mice, resulting in tumor inhibition. Moreover, strain HN_xs01 not only merely aggregated in the tumor environment, but also prevented pulmonary metastasis. It caused fragmentation of vessels and cell apoptosis, which contributed to its antitumor effect. In conclusion, X. stockiae HN_xs01 is a novel tumor-targeting strain with potential applications in medicinal and agricultural fields.

Phurealipids, produced by the entomopathogenic bacteria, Photorhabdus, mimic juvenile hormone to suppress insect immunity and immature development

Phurealipids (Photorhabdus urea lipids) are synthesized from Photorhabdus bacteria that are symbiotic to entomopathogenic nematodes. Their chemical structures are similar to that of juvenile hormone (JH) and have been suspected to mimic JH signaling in immunity and the development of insects. This study investigated the physiological roles of phurealipids with respect to their contribution to bacterial pathogenicity using four natural (HB13, HB69, HB416, and HB421) and one derivative (HB27) compound. First, phurealipids like JH suppressed insect immune responses. Overall, phurealipids showed JH like immunosuppressive behavior in a lepidopteran insect Spodoptera exigua larvae. More specifically, phurealipids significantly suppressed the hemocyte spreading behavior which is a key immune response upon immune challenge. Interestingly, the methyl urea derivatives (HB13, HB27, and HB69) were more potent than the unmethylated forms (HB416 and HB421). The inhibitory activity of phurealipids prevented the cellular immune response measured by hemocytic nodule formation in response to the bacterial challenge. Phurealipids also suppressed the expression of cecropin and gallerimycin, which are two highly inducible antimicrobial peptides, in S. exigua upon immune challenge. The immunosuppressive activity of the phurealipids significantly enhanced the bacterial pathogenicity of Bacillus thuringiensis against S. exigua. Second, phurealipids like JH prevented insect metamorphosis. Especially, the methylated urea derivatives of the phurealipids showed the JH-like function by inducing the expression of S. exigua Kr-h1, a transcriptional factor. At the pupal stage, exhibiting the lowest expression of Kr-h1, phurealipid treatments elevated the expression level of Kr-h1 and delayed the pupa-to-adult metamorphosis. These results suggest that phurealipids play crucial roles in Photorhabdus pathogenicity by suppressing host immune defenses and delaying host metamorphosis.

Microbial polyketides and their roles in insect virulence: from genomics to biological functions

Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.

Natural products from Photorhabdus and Xenorhabdus: mechanisms and impacts

Insects and fungal pathogens pose constant problems to public health and agriculture, especially in resource-limited parts of the world; and the use of chemical pesticides continues to be the main methods for the control of these organisms. Photorhabdus spp. and Xenorhabdus spp., (Fam; Morganellaceae), enteric symbionts of Steinernema, and Heterorhabditis nematodes are naturally found in soil on all continents, except Antarctic, and on many islands throughout the world. These bacteria produce diverse secondary metabolites that have important biological and ecological functions. Secondary metabolites include non-ribosomal peptides, polyketides, and/or hybrid natural products that are synthesized using polyketide synthetase (PRS), non-ribosomal peptide synthetase (NRPS), or similar enzymes and are sources of new pesticide/drug compounds and/or can serve as lead molecules for the design and synthesize of new alternatives that could replace current ones. This review addresses the effects of these bacterial symbionts on insect pests, fungal phytopathogens, and animal pathogens and discusses the substances, mechanisms, and impacts on agriculture and public health. KEY POINTS: • Insects and fungi are a constant menace to agricultural and public health. • Chemical-based control results in resistance development. • Photorhabdus and Xenorhabdus are compelling sources of biopesticides.

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters (BGCs) encoding the biosynthesis of many bioactive compounds, which are the basis for many important drugs used in human medicine. However, the association between BGCs and other functions encoded in the genomes of producers have remained elusive. Here, we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular BGC. We analyzed 3,889 enterobacterial genomes and found 13,266 BGCs, represented by 252 distinct BGC families and 347 additional singletons. A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory functions. The presented workflow opens up the possibility to discover novel secondary metabolites, better understand their physiological roles, and provides a guide to identify and analyze BGC associated gene sets.

Mutasynthetic Production and Antimicrobial Characterization of Darobactin Analogs

There is great need for therapeutics against multidrug-resistant, Gram-negative bacterial pathogens. Recently, darobactin A, a novel bicyclic heptapeptide that selectively kills Gram-negative bacteria by targeting the outer membrane protein BamA, was discovered. Its efficacy was proven in animal infection models of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, thus promoting darobactin A as a promising lead compound. Originally discovered from members of the nematode-symbiotic genus Photorhabdus, the biosynthetic gene cluster (BGC) encoding the synthesis of darobactin A can also be found in other members of the class Gammaproteobacteria. Therein, the precursor peptides DarB to -F, which differ in their core sequence from darobactin A, were identified in silico. Even though production of these analogs was not observed in the putative producer strains, we were able to generate them by mutasynthetic derivatization of a heterologous expression system. The analogs generated were isolated and tested for their bioactivity. The most potent compound, darobactin B, was used for cocrystallization with the target BamA, revealing a binding site identical to that of darobactin A. Despite its potency, darobactin B did not exhibit cytotoxicity, and it was slightly more active against Acinetobacter baumannii isolates than darobactin A. Furthermore, we evaluated the plasma protein binding of darobactin A and B, indicating their different pharmacokinetic properties. This is the first report on new members of this new antibiotic class, which is likely to expand to several promising therapeutic candidates. IMPORTANCE Therapeutic options to combat Gram-negative bacterial pathogens are dwindling with increasing antibiotic resistance. This study presents a proof of concept for the heterologous-expression approach to expand on the novel antibiotic class of darobactins and to generate analogs with different activities and pharmacokinetic properties. In combination with the structural data of the target BamA, this approach may contribute to structure-activity relationship (SAR) data to optimize inhibitors of this essential outer membrane protein of Gram-negative pathogens.

Efficacy of the Applied Natural Enemies on the Survival of Colorado Potato Beetle Adults

Simple Summary

Colorado potato beetle (CPB) Leptinotarsa decemlineata is the potato plant’s most destructive pest. Recently, resistance to the traditional insecticides has appeared, thus new environmentally friendly control agents are highly needed. In our study, we searched for the most effective entomopathogenic agents that could be used to decrease the emergence of CPB adults from the soil. We selected two entomopathogenic nematodes (Steinernema carpocapsae and S. feltiae) and one strain of fungus (Beauveria bassiana). The suspension application was done on the leaves, plus by watering the pods and the field plots. All the treatments had an obvious effect, but in the field, only the fungal treatment showed a promising result. Further research is needed to develop the most effective application for field usage.

Abstract

Colorado potato beetle Leptinotarsa decemlineata is among the most destructive pests of potatoes quickly developing resistance to traditional insecticides. In the present study, we tested the effect of various species and strains of entomopathogenic nematodes on CPB adults, and subsequently, the most effective nematodes were applied alone and in combination with entomopathogenic fungus B. bassiana in pots with potato plants and in the field and their effect on the number of emerging adults was evaluated. In the experimental infections, both the nematode invasion and pathogenicity were variable, and, in several strains, the mortality reached 100%. In pot experiments, soil application of nematodes S. carpocapsae 1343 and S. feltiae Jakub and fungus significantly decreased numbers of emerging CPB adults, while, after the application on leaves, only fungal treatment was effective. The field application of fungus B. bassiana significantly decreased the number of emerging CPB adults in comparison to control sites by ca. 30% while the effect of nematodes and the nematodes–fungus combination was not significant. In conclusion, we demonstrate the necessity of thorough bioassays to select the most effective nematode strains. Entomopathogenic nematodes have the potential to effectively decrease the emergence of CPB adults, but further research is needed to improve the effectiveness in the field.

Multi-locus phylogenetic analyses uncover species boundaries and reveal the occurrence of two new entomopathogenic nematode species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp

Species of the nematode genus Heterorhabditis are important biological control agents against agricultural pests. The taxonomy of this group is still unclear as it currently relies on phylogenetic reconstructions based on a few genetic markers with little resolutive power, specially of closely related species. To fill this knowledge gap, we sequenced several phylogenetically relevant genetic loci and used them to reconstruct phylogenetic trees, to calculate sequence similarity scores, and to determine signatures of species- and population-specific genetic polymorphism. In addition, we revisited the current literature related to the description, synonymisation, and declaration as species inquirendae of Heterorhabditis species to compile taxonomically relevant morphological and morphometric characters, characterized new nematode isolates at the morphological and morphometrical level, and conducted self-crossing and cross-hybridization experiments. The results of this study show that the sequences of the mitochondrial cytochrome C oxidase subunit I (COI) gene provide better phylogenetic resolutive power than the sequences of nuclear rRNA genes and that this gene marker can phylogenetically resolve closely related species and even populations of the same species with high precision. Using this gene marker, we found two new species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp. A detailed characterization of these species at the morphological and morphometric levels and nematode reproduction assays revealed that the threshold for species delimitation in this genus, using COI sequences, is 97% to 98%. Our study illustrates the importance of rigorous morphological and morphometric characterization and multi-locus sequencing for the description of new species within the genus Heterorhabditis, serves to clarify the phylogenetic relationships of this important group of biological control agents, and can inform future species descriptions to advance our efforts towards developing more tools for sustainable and environmentally friendly agriculture.

Photorhabdus hindustanensis sp. nov., Photorhabdus akhurstii subsp. akhurstii subsp. nov., and Photorhabdus akhurstii subsp. bharatensis subsp. nov., isolated from Heterorhabditis entomopathogenic nematodes

Two Gram-negative, rod-shaped bacteria, H1^T and H3^T, isolated from the digestive tract of Heterorhabditis entomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic positions. The 16S rRNA gene sequences of these strains indicate that they belong to the Gammaproteobacteria, to the family Morganellaceae, and to the Photorhabdus genus. Deeper analyses using whole genome-based phylogenetic reconstructions show that strains H1^T and H3^T are closely related to P. akhurstii DSM 15138^T, to P. hainanensis DSM 22397^T, and to P. namnaonensis PB45.5^T. In silico genomic comparisons confirm these observations and show that strain H1^T shares 70.6, 66.8, and 63.5 % digital DNA-DNA hybridization (dDDH) with P. akhurstii DSM 15138^T, P. hainanensis DSM 22397^T, and P. namnaonensis PB45.5^T, respectively, and that strain H3^T shares 76.6, 69.4, and 59.2 % dDDH with P. akhurstii DSM 15138^T, P. hainanensis DSM 22397^T, and P. namnaonensis PB45.5^T, respectively. Physiological and biochemical characterization reveals that these two strains differ from most of the validly described Photorhabdus species and from their more closely related taxa. Given the clear phylogenetic separations, that the threshold to discriminate species and subspecies is 70 and 79% dDDH, respectively, and that strains H1^T and H3^T differ physiologically and biochemically from their more closely related taxa, we propose to classify H1^T and H3^T into new taxa as follows: H3^T as a new subspecies within the species P. akhurstii, and H1^T as a new species within the Photorhabdus genus, in spite that H1^T shares 70.6 % dDDH with P. akhurstii DSM 15138^T, score that is slightly higher than the 70 % threshold that delimits species boundaries. The reason for this is that H1^T and P. akhurstii DSM 15138^T cluster apart in the phylogenetic trees and that dDDH scores between strain H1^T and other P. akhurstii strains are lower than 70 %. Hence, the following names are proposed: Photorhabdus hindustanensis sp. nov. with the type strain H1^T (=IARI-SGMG3^T,=KCTC 82683^T=CCM 9150^T=CCOS 1975^T) and P. akhurstii subsp. bharatensis subsp. nov. with the type strain H3^T (=IARI-SGHR2^T=KCTC 82684^T=CCM 9149^T=CCOS 1976^T). These propositions automatically create P. akhurstii subsp. akhurstii subsp. nov. with DSM 15138^T as the type strain (currently classified as P. akhurstii).

CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria

With the advent of genome sequencing and mining technologies, secondary metabolite biosynthetic gene clusters (BGCs) within bacterial genomes are becoming easier to predict. For subsequent BGC characterization, clustered regularly interspaced short palindromic repeats (CRISPR) has contributed to knocking out target genes and/or modulating their expression; however, CRISPR is limited to strains for which robust genetic tools are available. Here we present a strategy that combines CRISPR with chassis-independent recombinase-assisted genome engineering (CRAGE), which enables CRISPR systems in diverse bacteria. To demonstrate CRAGE-CRISPR, we select 10 polyketide/non-ribosomal peptide BGCs in Photorhabdus luminescens as models and create their deletion and activation mutants. Subsequent loss- and gain-of-function studies confirm 22 secondary metabolites associated with the BGCs, including a metabolite from a previously uncharacterized BGC. These results demonstrate that the CRAGE-CRISPR system is a simple yet powerful approach to rapidly perturb expression of defined BGCs and to profile genotype-phenotype relationships in bacteria.

At the Crossroads of Bioenergetics and Antibiotic Discovery

Dr. Vladimir Skulachev was my mentor, and his pioneering work in the field of bioenergetics inspired the discoveries described in this review, written in the form of a personal account of events. Examining basic mechanisms of chemiosmotic coupling unexpectedly led us to transenvelope multidrug resistance pumps (MDR pumps) that severely limit development of novel antibiotics. One of the major advances of Skulachev and his group was the discovery of the mitochondrial membrane potential with the use of permeant cations such as TPP⁺, which served as electric probes. We describe our finding of their natural counterparts in plants, where they act as antimicrobials. The most challenging problems in antimicrobial drug discovery are antibiotic tolerance of chronic infections caused by dormant persister cells; antibiotic resistance, responsible for the current antimicrobial resistance crisis (AMR); and finding novel compounds acting against Gram-negative bacteria, protected by their powerful multidrug resistance pumps. Our study of persisters shows that these are rare cells formed by stochastic fluctuation in expression of Krebs cycle enzymes, leading to a drop in ATP, target shutdown, and antibiotic tolerance. Searching for compounds that can corrupt targets in the absence of ATP, we identified acyldepsipeptide (ADEP) that activates the ClpP protease, forcing cells to self-digest. Growing previously uncultured bacteria led us to teixobactin, a novel cell wall acting antibiotic. Teixobactin avoids efflux by targeting lipid II and lipid III, precursors of peptidoglycan and wall teichoic acid, located on the surface. The targets are immutable, and teixobactin is the first antibiotic with no detectable resistance. Our search for compounds acting against Gram-negative bacteria led to the discovery of darobactins, which also hit a surface target, the essential chaperone BamA.

Structure and biosynthesis of sorangipyranone - a new γ-dihydropyrone from the myxobacterial strain MSr12020

Sorangipyranone was isolated as a novel natural product featuring a unique 2,3-dihydro-γ-4H-pyrone scaffold from cultures of the myxobacterial strain MSr12020. We report here the full structure elucidation of sorangipyranone by spectroscopic techniques including 2D NMR and high-resolution mass spectrometry together with the analysis of the biosynthetic pathway. Determination of the absolute configuration was performed by time-dependent density functional theory-electronic circular dichroism calculations and determination of the applicability of the Snatzke's helicity rule, to correlate the high-wavelength n→π* electronic circular dichroism (ECD) transition and the absolute configuration of the 2,3-dihydro-4H-γ-pyrone, was done by the analysis of low-energy conformers and the Kohn-Sham orbitals. Sorangipyranone outlines a new class of a γ-dihydropyrone-containing natural product comprised of malonyl-CoA-derived building blocks and features a unique polyketide scaffold. In silico analysis of the genome sequence of the myxobacterial strain MSr12020 complemented with feeding experiments employing stable isotope-labeled precursors allowed the identification and annotation of a candidate biosynthetic gene cluster that encodes a modular polyketide synthase assembly line. A model for the biosynthetic pathway leading to the formation of the γ-dihydropyrone scaffold is presented in this study.

Interactions of host-associated multispecies bacterial communities

The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.

Natural products in drug discovery: advances and opportunities

Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.

Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host

Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.

Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens)

Covering: up to the second quarter of 2020 Threat or treat? While pathogenic bacteria pose significant threats, they also represent a huge reservoir of potential pharmaceuticals to treat various diseases. The alarming antimicrobial resistance crisis and the dwindling clinical pipeline urgently call for the discovery and development of new antibiotics. Pathogenic bacteria have an enormous potential for natural products drug discovery, yet they remained untapped and understudied. Herein, we review the specialised metabolites isolated from entomopathogenic, phytopathogenic, and human pathogenic bacteria with antibacterial and antifungal activities, highlighting those currently in pre-clinical trials or with potential for drug development. Selected unusual biosynthetic pathways, the key roles they play (where known) in various ecological niches are described. We also provide an overview of the mode of action (molecular target), activity, and minimum inhibitory concentration (MIC) towards bacteria and fungi. The exploitation of pathogenic bacteria as a rich source of antimicrobials, combined with the recent advances in genomics and natural products research methodology, could pave the way for a new golden age of antibiotic discovery. This review should serve as a compendium to communities of medicinal chemists, organic chemists, natural product chemists, biochemists, clinical researchers, and many others interested in the subject.

Variations of Indole Metabolites and NRPS-PKS Loci in Two Different Virulent Strains of Xenorhabdus hominickii

Xenorhabdus hominickii ANU1 is known to be an entomopathogenic bacterium symbiotic to nematode Steinernema monticolum. Another bacterial strain X. hominickii DY1 was isolated from a local population of S. monticolum. This bacterial strain X. hominickii DY1 was found to exhibit high insecticidal activities against lepidopteran and coleopteran species after hemocoelic injection. However, these two X. hominickii strains exhibited significant variations in insecticidal activities, with ANU1 strain being more potent than DY1 strain. To clarify their virulence difference, bacterial culture broths of these two strains were compared for secondary metabolite compositions. GC-MS analysis revealed that these two strains had different compositions, including pyrrolopyrazines, piperazines, cyclopeptides, and indoles. Some of these compounds exhibited inhibitory activities against phospholipase A₂ to block eicosanoid biosynthesis and induce significant immunosuppression. They also exhibited significant insecticidal activities after oral feeding, with indole derivatives being the most potent. More kinds of indole derivatives were detected in the culture broth of ANU1 strain. To investigate variations in regulation of secondary metabolite production, expression level of leucine-responsive regulatory protein (Lrp), a global transcription factor, was compared. ANU1 strain exhibited significantly lower Lrp expression level than DY1 strain. To assess genetic variations associated with secondary metabolite synthesis, bacterial loci encoding non-ribosomal protein synthase and polyketide synthase (NRPS-PKS) were compared. Three NRPS and four PKS loci were predicted from the genome of X. hominickii. The two bacterial strains exhibited genetic variations (0.12∼0.67%) in amino acid sequences of these NRPS-PKS. Most NRPS-PKS genes exhibited high expression peaks at stationary phase of bacterial growth. However, their expression levels were significantly different between the two strains. These results suggest that differential virulence of the two bacterial strains is caused by the difference in Lrp expression level, leading to difference in the production of indole compounds and other NRPS-PKS-associated secondary metabolites.

Virulent secondary metabolites of entomopathogenic bacteria genera, Xenorhabdus and Photorhabdus, inhibit phospholipase A2 to suppress host insect immunity

BACKGROUND

Xenorhabdus and Photorhabdus are entomopathogenic bacteria that cause septicemia and toxemia in insects. They produce secondary metabolites to induce host immunosuppression. Their metabolite compositions vary among bacterial species. Little is known about the relationship between metabolite compositions and the bacterial pathogenicity. The objective of this study was to compare pathogenicity and production of secondary metabolites of 14 bacterial isolates (species or strains) of Xenorhabdus and Photorhabdus.

RESULTS

All bacterial isolates exhibited insecticidal activities after hemocoelic injection to Spodoptera exigua (a lepidopteran insect) larvae, with median lethal doses ranging from 168.8 to 641.3 CFU per larva. Bacterial infection also led to immunosuppression by inhibiting eicosanoid biosynthesis. Bacterial culture broth was fractionated into four different organic extracts. All four organic extracts of each bacterial species exhibited insecticidal activities and resulted in immunosuppression. These organic extracts were subjected to GC-MS analysis which predicted 182 compounds, showing differential compositions for 14 bacteria isolates. There were positive correlations between total number of secondary metabolites produced by each bacterial culture broth and its bacterial pathogenicity based on immunosuppression and insecticidal activity. From these correlation results, 70 virulent compounds were selected from secondary metabolites of high virulent bacterial isolates by deducting those of low virulent bacterial isolates. These selected virulent compounds exhibited significant immunosuppressive activities by inhibiting eicosanoid biosynthesis. They also exhibited relatively high insecticidal activities.

CONCLUSION

Virulence variation between Xenorhabdus and Photorhabdus is determined by their different compositions of secondary metabolites, of which PLA2 inhibitors play a crucial role.

Improving the Yield of Xenocoumacin 1 Enabled by In Situ Product Removal

Xenocoumacin 1 (Xcn1), a major antimicrobial compound produced by Xenorhabdus nematophila CB6, has great potential to be developed into a novel biofungicide. However, its low yield in the producing cells has limited its possible commercial applications. In this study, we explored the effect of in situ product removal (ISPR), a well-established recovery technique, with the use of macroporous resin X-5 on the production of Xcn1 in a fermentation setting. Relative to the routine fermentation process, the yield of Xcn1 was improved from 42.5 to 73.8 μg/mL (1.7-fold) and 12.9 to 60.3 μg/mL (4.7-fold) in three and ten days, respectively. By agar diffusion plate and growth inhibition assays, the antibiotic activity against Bacillus subtilis and Alternaria solani was also found to be improved. Further study revealed that protection of Xcn1 against degradation and decrease in cell self-toxicity as well as upregulation of biosynthesis-related genes of Xcn1 at the transcription level contributed to yield improvement of Xcn1. In addition, resin X-5 significantly altered the metabolite profile of X. nematophila CB6, which could promote the discovery of new antibiotics.

Tolerance of the mealworm beetle, Tenebrio molitor, to an entomopathogenic nematode, Steinernema feltiae, at two infection foci, the intestine and the hemocoel

An entomopathogenic nematode, Steinernema feltiae K1, exhibits pathogenicity in various insect hosts, however, its virulence among the target insect species varies. Specifically, a coleopteran insect, Tenebrio molitor, is less susceptible to S. feltiae than are lepidopteran insects. We analyzed the low virulence of S. feltiae against T. molitor sequentially, in entering the gut lumen and penetrating the hemocoel, and in hemocoelic immune defenses by comparing the responses to those of a lepidopteran insect, Spodoptera exigua. Infective juveniles (IJs) of S. feltiae exhibited higher virulence and produced more progeny IJs in S. exigua than in T. molitor. The difference in IJ behavior was observed in the IJ invasion rate (IJs in gut lumen/IJs treated) after treatment, in which a lower rate was observed in T. molitor (20.4%) than in S. exigua (55.5%). Also, a lower hemocoelic penetration rate of IJs (IJs in hemocoel/IJs in gut) was observed in T. molitor (54%) than in S. exigua (74%) 24 h after feeding treatment. To investigate the immune defense in the hemocoel, insect hemolymph samples were incubated with IJs. The encapsulation behavior and phenoloxidase activity was higher in T. molitor hemolymph than in S. exigua hemolymph, which resulted in a significantly higher nematicidal activity in S. exigua. The humoral immune responses against S. feltiae were also different between the two species. The expression of two antimicrobial peptides, cecropin and attacin 1, was much higher in T. molitor. Furthermore, eicosanoid biosynthetic activity against S. feltiae was different in the two host species; sPLA₂ activity was highly inducible in T. molitor but not in S. exigua. These results suggest that variability of the immune defense in the target insects, as well as in the invasion and penetration rates of IJs to the hemocoel, plays a crucial role in determining the insecticidal virulence of S. feltiae.

Evolution and taxonomy of nematode-associated entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus: an overview

Entomopathogenic bacteria from the genera Photorhabdus and Xenorhabdus are closely related Gram-negative bacilli from the family Enterobacteriaceae (γ-Proteobacteria). They establish obligate mutualistic associations with soil nematodes from the genera Steinernema and Heterorhabditis to facilitate insect pathogenesis. The research of these two bacterial genera is focused mainly on their unique interactions with two different animal hosts, i.e. nematodes and insects. So far, studies of the mutualistic bacteria of nematodes collected from around the world have contributed to an increase in the number of the described Xenorhabdus and Photorhabdus species. Recently, the classification system of entomopatogenic nematode microsymbionts has undergone profound revision and now 26 species of the genus Xenorhabdus and 19 species of the genus Photorhabdus have been identified. Despite their similar life style and close phylogenetic origin, Photorhabdus and Xenorhabdus bacterial species differ significantly in e.g. the nematode host range, symbiotic strategies for parasite success, and arrays of released antibiotics and insecticidal toxins. As the knowledge of the diversity of entomopathogenic nematode microsymbionts helps to enable the use thereof, assessment of the phylogenetic relationships of these astounding bacterial genera is now a major challenge for researchers. The present article summarizes the main information on the taxonomy and evolutionary history of Xenorhabdus and Photorhabdus, entomopathogenic nematode symbionts.

Phenylethylamides derived from bacterial secondary metabolites specifically inhibit an insect serotonin receptor

Serotonin (5-hydroxytryptamine: 5-HT) is a biogenic monoamine that mediates immune responses and modulates nerve signal in insects. Se-5HTR, a specific receptor of serotonin, has been identified in the beet armyworm, Spodoptera exigua. It is classified into subtype 7 among known 5HTRs. Se-5HTR was expressed in all developmental stages of S. exigua. It was expressed in all tested tissues of larval stage. Its expression was up-regulated in hemocytes and fat body in response to immune challenge. RNA interference (RNAi) of Se-5HTR exhibited significant immunosuppression by preventing cellular immune responses such as phagocytosis and nodulation. Treatment with an inhibitor (SB-269970) specific to 5HTR subtype 7 resulted in significant immunosuppression. Furthermore, knockout mutant of Se-5HTR by CRISPR-Cas9 led to significant reduction of phagocytotic activity of S. exigua hemocytes. Such immunosuppression was also induced by bacterial secondary metabolites derived from Xenorhabdus and Photorhabdus. To determine specific bacterial metabolites inhibiting Se-5HTR, this study screened 37 bacterial secondary metabolites with respect to cellular immune responses associated with Se-5HTR and selected 10 potent inhibitors. These 10 selected compounds competitively inhibited cellular immune responses against 5-HT and shared phenylethylamide (PEA) chemical skeleton. Subsequently, 46 PEA derivatives were screened and resulting potent chemicals were used to design a compound to be highly inhibitory against Se-5HTR. The designed compound was chemically synthesized. It showed high immunosuppressive activities along with specific and competitive inhibition activity for Se-5HTR. This study reports the first 5HT receptor from S. exigua and provides its specific inhibitor designed from bacterial metabolites and their derivatives.

A new antibiotic selectively kills Gram-negative pathogens

The current need for novel antibiotics is especially acute for drug-resistant Gram-negative pathogens^1,2. These microorganisms have a highly restrictive permeability barrier, which limits penetration of most compounds^3,4. As a result, the last class of antibiotics acting against Gram-negative bacteria was developed in the 60s². We reason that useful compounds can be found in bacteria that share similar requirements for antibiotics with humans, and focus on Photorhabdus symbionts of entomopathogenic nematode microbiomes. Here we report a new antibiotic that we name darobactin, from a screen of Photorhabdus isolates. Darobactin is coded by a silent operon with little production under laboratory conditions, and is ribosomally synthesized. Darobactin has an unusual structure with two fused rings that form post-translationally. The compound is active against important Gram-negative pathogens both in vitro and in animal models of infection. Mutants resistant to darobactin map to BamA, an essential chaperone and translocator that folds outer membrane proteins. Our study suggests that bacterial symbionts of animals harbor antibiotics that are particularly suitable for development into therapeutics.

In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites

In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery.

Variation in pathogenicity of different strains of Xenorhabdus nematophila; Differential immunosuppressive activities and secondary metabolite production

Xenorhabdus nematophila, an entomopathogenic bacterium, is mutualistic with the nematode Steinernema carpocapsae. The bacterium produces secondary metabolites to inhibit target insect phospholipase A₂ (PLA₂) and induce immunosuppression, which is required for the pathogenicity of this bacterium-nematode complex. However, it was unclear if immunosuppressive intensity of the bacteria was correlated with their insecticidal potency. We compared six different X. nematophila strains inhibiting the immune responses of the beet armyworm (Spodoptera exigua) to explain their virulence variations. In addition to four known strains obtained from the Korean Agricultural Culture Collection, we identified two new strains (SK1 and SK2) of X. nematophila from two different isolates of S. carpocapsae. Although all six strains were virulent, they showed significant variation in median lethal bacterial dosage (LD₅₀). The LD₅₀ of most strains was 15-30 CFU/larva, however, the LD₅₀ of the SK1 strain was more than two-fold higher against S. exigua larvae. Immunosuppressive activities of the six strains were measured by comparing hemocyte-spreading behavior and nodule formation; the SK1 strain was significantly less potent than other bacterial strains. These suppressed hemocyte behaviors were recovered by adding arachidonic acid (a catalytic product of PLA₂) into all six strains. Bacterial culture broth was fractionated with different organic solvents and the ability to inhibit immune response and PLA₂ activity were assessed. All organic extracts had immunosuppressive activities and PLA₂-inhibitory activities. GC-MS analysis showed that these organic extracts possessed a total of 87 different compounds. There were variations in chemical components among the six bacterial strains. Organic extracts of SK1 strain, which exhibited the lowest virulence, contained the least number of secondary metabolites.

Cyclo(tetrahydroxybutyrate) production is sufficient to distinguish between Xenorhabdus and Photorhabdus isolates in Thailand

Bacteria of the genera Photorhabdus and Xenorhabdus produce a plethora of natural products to support their similar symbiotic life cycles. For many of these compounds, the specific bioactivities are unknown. One common challenge in natural product research when trying to prioritize research efforts is the rediscovery of identical (or highly similar) compounds from different strains. Linking genome sequence to metabolite production can help in overcoming this problem. However, sequences are typically not available for entire collections of organisms. Here, we perform a comprehensive metabolic screening using HPLC-MS data associated with a 114-strain collection (58 Photorhabdus and 56 Xenorhabdus) across Thailand and explore the metabolic variation among the strains, matched with several abiotic factors. We utilize machine learning in order to rank the importance of individual metabolites in determining all given metadata. With this approach, we were able to prioritize metabolites in the context of natural product investigations, leading to the identification of previously unknown compounds. The top three highest ranking features were associated with Xenorhabdus and attributed to the same chemical entity, cyclo(tetrahydroxybutyrate). This work also addresses the need for prioritization in high-throughput metabolomic studies and demonstrates the viability of such an approach in future research.