Search Results (122)

Anaerobes, the oldest evolutionary life forms, have been unexplored for their potential to produce secondary metabolites due to the difficulties observed in their cultivation. Antimicrobials derived from anaerobic bacteria are an emerging and valuable source of novel therapeutic agents. The urgent need for new antimicrobial agents due to rising antibiotic resistance has prompted an investigation into anaerobic bacteria. The conventional method of antimicrobial discovery is based on cultivation and extraction methods. Antibacterial and antifungal substances are produced by anaerobic bacteria, but reports are limited due to oxygen-deficient growth requirements. The genome mining approach revealed the presence of biosynthetic gene clusters involved in various antimicrobial compound synthesis. Thus, the current review is focused on antimicrobials derived from anaerobes to unravel the potential of anaerobic bacteria as an emerging valuable source of therapeutic agents. These substances frequently consist of peptides, lipopeptides, and other secondary metabolites. Many of these antimicrobials have distinct modes of action that may be able to go around established resistance pathways. To this effect, we discuss diverse antimicrobial compounds produced by anaerobic bacteria, their biosynthesis, heterologous production, and activity. The findings suggest that anaerobic bacteria harbor significant biosynthetic potential, warranting further exploration through recombinant production for developing new antibiotics. Full article

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232^T (98.9%) and Lentzea flava NBRC 15743^T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54^T and these related strains were below the thresholds for species delineation. Strain E54^T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H₄), and major fatty acids included iso-C_16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54^T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54^T as a novel species. The strain E54^T (=JCM 34936^T = GDMCC 4.216^T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article

Peptaibols are linear fungal peptides featuring α,α-dialkylated amino acids (e.g., α-aminoisobutyric acid (Aib), isovaline (Iva)) and characteristic C-terminal alcohol groups. Despite their promising antibacterial and antiplasmodial activities, detailed biosynthetic studies remain limited. A genome-guided study of the fungus Trichodema sp. SK1-7, isolated from decaying wood, revealed the production of previously described trichorozin IV (1), along with novel SF4-type peptaibol 2 (trichorozin V). The structures of these compounds were elucidated through MS analysis, NMR study and advanced Marfey’s method. The genome of Trichoderma sp. SK1-7 harbors two PKS-NRPS hybrid gene clusters containing 14 and 18 adenylation domains. Analysis of the modular architecture suggested that trichorozins are synthesized by a 14-module protein via a module skipping mechanism. Genome mining revealed several types of short peptaibol synthase architectures (10–14 adenylation domains) across various Trichoderma species, accompanied by similar long peptaibol synthases. Furthermore, putative Aib/Iva biosynthesis machinery in Trichoderma was identified, showing specific architectures potentially involved in regulating peptaibol biosynthesis. Feeding experiments demonstrated that peptaibol production depends on the ratio of Iva/Aib. The isolated compounds exhibited moderate antibacterial and cytotoxic activities along with a synergistic effect when combined with membrane-targeting antibiotics. Our findings suggest that genome-guided approaches hold promise for further development of peptabiotics with a wide range of applications, including antibiotic adjuvants. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article

The growing threat of antibiotic resistance has made treating bacterial and fungal infections increasingly difficult. With the discovery of new antibiotics slowing down, alternative strategies are urgently needed. Siderophores, small iron-chelating molecules produced by microorganisms, play a crucial role in iron acquisition and serve as virulence factors in many pathogens. Because iron is essential for microbial survival, targeting siderophore biosynthesis and transport presents a promising approach to combating drug-resistant infections. This review explores the key genetic and biochemical mechanisms involved in siderophore production, emphasizing potential drug targets within these pathways. Three major biosynthetic routes are examined: nonribosomal peptide synthetase (NRPS)-dependent, polyketide synthase (PKS)-based, and NRPS-independent (NIS) pathways. Additionally, microbial iron uptake mechanisms and membrane-associated transport systems are discussed, providing insights into their role in sustaining pathogenic growth. Recent advances in inhibitor development have shown that blocking critical enzymes in siderophore biosynthesis can effectively impair microbial growth. By disrupting these pathways, new antimicrobial strategies can be developed, offering alternatives to traditional antibiotics and potentially reducing the risk of resistance. A deeper understanding of siderophore biosynthesis and its regulation not only reveals fundamental microbial processes but also provides a foundation for designing targeted therapeutics. Leveraging these insights could lead to novel drugs that overcome antibiotic resistance, offering new hope in the fight against persistent infections. Full article

Nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) play crucial roles in the development and pathogenicity of the entomopathogenic fungus Beauveria bassiana. However, they are among the few biosynthetic gene clusters with unknown functions in B. bassiana. To investigate the role of the hybrid PKS–NRPS synthetase gene BBA_09856 in B. bassiana, we constructed a mutant strain, ∆BBA09856-WT, by deleting the BBA_09856 gene through Agrobacterium-mediated transformation. We then analyzed the biological characteristics of the mutant strain and the virulence of the mutant strain toward Ostrinia furnacalis larvae, as well as its antagonistic effects against the phytopathogen Botrytis cinerea. We found that the average growth rate of the three mutant strains, ∆BBA09856-WT, was significantly higher compared to the wild-type (WT) strain on the 15th day of culture on potato dextrose agar (PDA) plates (7.01 cm vs. 6.30 cm, p < 0.01). Additionally, the average spore production(3.16 × 10⁷/cm² vs. 9.95 × 10⁶/cm², p < 0.001) and germination rate (82.50% vs. 54.72%, 12 h, p < 0.001) were significantly different between the three mutant strains, ∆BBA09856-WT, and the WT strain. The average survival rates of O. furnacalis infected with the WT strain and the three mutant strains, ∆BBA09856-WT, after 8 days were 61.66%, and 30.00%, respectively, indicating that the pathogenicity of the tested mutant strains was significantly greater than that of the WT strain. The results of the dual culture test indicated that the inhibitory rates of the WT and ∆BBA09856-WT strains against B. cinerea were 40.25% and 47.65%, respectively (p < 0.001). Similarly, in the dual culture test, the WT strain reduced the growth of B. cinerea by 9.90%, while the ∆BBA09856-WT exhibited a significantly greater inhibition rate of 28.29% (p < 0.05). The diameters of disease spots, measured 6 d after inoculation with B. cinerea in the tomato treatment groups, revealed significant differences in endophytic colonization between the WT and ∆BBA09856-WT strains in the WT+Bc and ∆BBA09856-WT+Bc treatment groups (15.26 mm vs. 12.16 mm, p < 0.01). Notably, ∆BBA09856-WT exhibited enhanced virulence toward O. furnacalis larvae and increased antagonistic activity against B. cinerea. Our results indicate that the gene BBA_09856 may have a negative correlation with the development and virulence of B. bassiana toward the insect pest O. furnacalis larvae, as well as its antagonism against B. cinerea. These findings suggest that molecular techniques, such as gene editing, could be employed to develop superior strains of B. bassiana for the biological control of plant diseases and insect pests. Full article

Bark beetle-associated bacteria from the sub-boreal and boreal forests of northern Canada represent a largely unexplored source of bioactive natural products. This study aims to investigate the chemical potential of bacteria isolated from Dendroctonus ponderosae, Dendroctonus rufipennis, Dendroctonus pseudotsugae, and Ips perturbatus by focusing on nitrogen-containing secondary metabolites. Genomic analyses of the bacterial isolates identified diverse biosynthetic gene clusters (BGCs), including nonribosomal peptides (NRPs), NRPS-PKS hybrids, and ribosomally synthesized and post-translationally modified peptides (RiPPs), many of which exhibit low sequence homology, suggesting potential for novel bioactive compounds. Nitrogen-15 NMR spectroscopy was employed to detect nitrogen-containing functional groups in crude extracts, revealing distinct signals for amides, amines, and nitrogen heterocycles. The combination of BGC predictions and NMR data highlighted the genetic and chemical diversity of these bacteria and underscored the potential for discovering novel nitrogen-rich metabolites. These findings provide a foundation for further exploration of bioactive natural products with pharmaceutical and agrochemical applications and potential to contribute to the understanding of the chemical ecology of bark beetle–microbe interactions in northern ecosystems. Full article

This study presents the first comprehensive genomic analysis of Cryptoporus qinlingensis, a classical folk medicine and newly identified macrofungus from the Qinling Mountains. Utilizing advanced sequencing technologies, including PacBio HiFi and Hi-C, we achieved a high-quality chromosome-level genome assembly. The genome, sized at 39.1 Mb, exhibits a heterozygosity of 0.21% and contains 21.2% repetitive sequences. Phylogenetic analysis revealed a recent divergence of C. qinlingensis from Dichomitus squalens approximately 212.26 million years ago (MYA), highlighting the rapid diversification within the Polyporaceae family. Comparative genomic studies indicate significant gene family contraction in C. qinlingensis, suggesting evolutionary adaptations. The identification of a tetrapolar mating system, along with the analysis of CAZymes and P450 genes, underscores the genomic complexity and ecological adaptability of this species. Furthermore, the discovery of 30 biosynthetic gene clusters (BGCs) related to secondary metabolites, including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and terpene synthesis enzymes, opens new avenues for exploring bioactive compounds with potential medicinal applications. This research not only enriches our understanding of the Cryptoporus genus but also provides a valuable foundation for future studies aiming to harness the therapeutic potential of C. qinlingensis and to further explore its ecological and evolutionary significance. Full article

Fungal secondary metabolism (SM) is highly correlated with physiological processes that are typically regulated by pleiotropic regulators. In this study, we purposefully altered PratfA, a crucial regulator associated with oxidative stress in Penicillium raistrickii CGMCC 3.1066. After the knockout of PratfA, a novel polyketide (PK) raistrilide A (1) and the known nonribosomal peptide (NRP) tunicoidine (2) subsequently disappeared. Notably, compound 1 is a rare octaketone derivative and contains two unsubstituted cis-double bonds, demonstrating its unique biosynthetic mechanism. The knockout of PratfA resulted in the disappearance of 1–2 and greatly increased the susceptibility of ΔPratfA mutant strain to oxidative stress, rendering it nearly impossible to survive in such environments. At present, the OE⸬PratfA strain showed no phenotypic or oxidative stress sensitivity differences compared to the wild-type strain. Our findings highlight that the oxidative-stress-related transcription factor (TF) PratfA influences SM pathways in P. raistrickii. The manipulation of regulatory factors can guide the discovery of novel natural products (NPs). Full article

Irpex lacteus is an edible and medicinal macrofungus with significant biological activity and broad pharmaceutical prospects that has received increasing attention in recent years. Although it is an important resource for macrofungi, knowledge of it remains limited. In this study, we sequenced, de novo assembled, and annotated the whole genome of I. lacteus using a PacBio Sequel II sequencer. The assembled 41.83 Mb genome contains 13,135 predicted protein-coding genes, 83.44% of which have searchable sequence similarity to other genes available in public databases. Using genome-based bioinformatics analysis, we identified 556 enzymes involved in carbohydrate metabolism and 103 cytochrome P450 proteins. Genome annotation revealed genes for key enzymes responsible for the biosynthesis of secondary metabolites, such as terpenoids and polyketides. Among them, we identified 14 terpene synthases, 8 NRPS-like enzymes, and 4 polyketide synthases (PKS), as well as 2 clusters of biosynthetic genes presumably related to terpene synthesis in I. lacteus. Gene family analysis revealed that the MYB transcription factor gene family plays an important role in the growth and development of I. lacteus. This study further enriches the genomic content of I. lacteus, provides genomic information for further research on the molecular mechanism of I. lacteus, and promotes the development of I. lacteus in the fields of drug research and functional food production. Full article

Fungal secondary metabolites (SMs) have broad applications in biomedicine, biocontrol, and the food industry. In this study, whole-genome sequencing and annotation of Taiwanofungus gaoligongensis were conducted, followed by comparative genomic analysis with 11 other species of Polyporales to examine genomic variations and secondary metabolite biosynthesis pathways. Additionally, transcriptome data were used to analyze the differential expression of polyketide synthase (PKS), terpene synthase (TPS) genes, and transcription factors (TFs) under different culture conditions. The results show that T. gaoligongensis differs from other fungal species in genome size (34.58 Mb) and GC content (50.72%). The antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analysis reveals significant variation in the number of SM biosynthetic gene clusters (SMBGCs) across the 12 species (12–29), with T. gaoligongensis containing 25 SMBGCs: 4 PKS, 6 non-ribosomal peptide synthetase (NRPS), and 15 TPS clusters. The TgPKS1 gene is hypothesized to be involved in the biosynthesis of orsellinic acid or its derivatives, while TgPKS2 might catalyze the synthesis of 6-methylsalicylic acid (6MSA) and its derivatives. The TgTRI5 genes are suggested to synthesize tetracyclic sesquiterpene type B trichothecene compounds, while TgPentS may be involved in the synthesis of δ-cadinol, β-copaene, and α-murolene analogs or derivatives. Comparative genomic analysis shows that the genome size of T. gaoligongensis is similar to that of T. camphoratus, with comparable SMs. Both species share four types of PKS domains and five distinct types of TPS. Additionally, T. gaoligongensis exhibits a high degree of similarity to Laetiporus sulphureus, despite belonging to a different genus within the same family. Transcriptome analysis reveals significant variation in the expression levels of PKS and TPS genes across different cultivation conditions. The TgPKS1 and TgPKS4 genes, along with nine TgTFs, are significantly upregulated under three solid culture conditions. In contrast, under three different liquid culture conditions, the TgPKS3, TgTRI5-1, and TgTRI5-2 genes, along with twelve TgTFs, exhibit higher activity. Co-expression network analysis and TgTFs binding site prediction in the promoter regions of TgPKS and TgTPS genes suggest that TgMYB9 and TgFTD4 regulate TgPKS4 expression. TgHOX1, TgHSF2, TgHSF3, and TgZnF4 likely modulate TgPKS3 transcriptional activity. TgTRI5-1 and TgTRI5-5 expression is likely regulated by TgbZIP2 and TgZnF15, respectively. This study provides new insights into the regulatory mechanisms of SMs in T. gaoligongensis and offers potential strategies for enhancing the biosynthesis of target compounds through artificial intervention. Full article

In this paper, we present a novel class of hybrid polyketides, tenuazamines A–H (1–8), which exhibit a unique tautomeric equilibrium from Alternaria alternata FL7. The elucidation of the structures was achieved through a diverse combination of NMR, HR-ESIMS, and ECD methods, with a focus on extensive spectroscopic data analysis. Notably, compounds 1, 4, 8–9 exhibited potent toxic effects on the growth of Arabidopsis thaliana. This research expands the structural diversity of tenuazonic acid compounds derived from endophytic fungi and provides potential hit compounds for the development of herbicides. Full article

The swnH1 gene in the endophytic fungus Alternaria oxytropis OW 7.8 isolated from Oxytropis glabra was identified, and the gene knockout mutant ΔswnH1 was first constructed in this study. Compared with A. oxytropis OW 7.8, the ΔswnH1 mutant exhibited altered colony and mycelium morphology, slower growth rate, and no swainsonine (SW) in mycelia, indicating that the function of the swnH1 gene promoted SW biosynthesis. Five differential expressed genes (DEGs) closely associated with SW synthesis were identified by transcriptomic analysis of A. oxytropis OW 7.8 and ΔswnH1, with sac, swnR, swnK, swnN, and swnH2 down-regulating. Six differential metabolites (DEMs) closely associated with SW synthesis were identified by metabolomic analysis, with P450, PKS-NRPS, saccharopine, lipopolysaccharide kinase, L-PA, α-aminoadipic, and L-stachydrine down-regulated, while L-proline was up-regulated. The SW biosynthetic pathways in A. oxytropis OW 7.8 were predicted and refined. The results lay the foundation for in-depth exploration of the molecular mechanisms and metabolic pathways of SW synthesis in fungi and provide reference for future control of SW in locoweeds, which would benefit the development of animal husbandry and the sustainable use of grassland ecosystems. Full article

Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the first strain. To date, no whole-genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192-base circular chromosome with GC content of 52.68%. The annotation revealed the presence of 5605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41,400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of the secondary metabolites includes aminoglycosides, PKS, NRPS, PKS–NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized the butirosin BGCs previously studied in several N. circulans strains. Additionally, the comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41,400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, and Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provides insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggests the need for continued studies on butirosin biosynthesis from an enzymatic perspective. Full article

Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea’s pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea’s biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus’s secondary metabolism, with implications for biotechnology and crop disease management. Full article