Co-culture: stimulate the metabolic potential and explore the molecular diversity of natural products from microorganisms

Exploring the modern approaches to enhance fungal endophyte-derived bioactive secondary metabolites

Over the past few decades, microbial-derived bioactive compounds have been tested for antiviral, antimicrobial, and anticancer properties. In addition, fungal-derived bioactive secondary metabolites (SMs) are increasingly being suggested as suitable alternative sources of potent bioactive compounds. The development of suitable, precise in vitro and in vivo screening techniques may contribute to identifying the biochemical and physiological effects of compounds. This advancement in bioassay evaluation techniques helps identify potential bioactive microbes rapidly. The main obstacles, however, have been the production of insufficient amounts of chemicals, endophytes' attenuation or loss of ability to produce the molecule of interest when grown in cultures, and fungal endophytes' failure to exhibit their full biosynthetic potential in lab conditions. These have led to the use of small chemical elicitors that activate the silent biosynthetic gene clusters (BGCs) in fungi, causing epigenetic alterations that increase the amount of desired metabolites or trigger the synthesis of hitherto unknown compounds. The silent BGCs were activated to maximize production of bioactive secondary metabolites, thereby increasing the yield of desired compounds or triggering the synthesis of novel metabolites. Other strategies include gene knocking, inducing mutations, heterologous expression, one strain-many compounds (OSMAC), epigenetic modifications, etc. This review is focused on the mechanism of plant-microbe interaction in enhancing the biosynthesis of fungal metabolites along with the BGCs for the biosynthesis of the bioactive fungal metabolites. Furthermore, we also discuss the genomic mining approaches for BGCs, the role of ribosomal engineering, precursor feeding, and various elicitors to explore the structural diversity of novel bioactive compounds.

Unravelling fungal genome editing revolution: pathological and biotechnological application aspects

Fungi represent a broad and evolutionarily unique group within the eukaryotic domain, characterized by extensive ecological adaptability and metabolic versatility. Their inherent biological intricacy is evident in the diverse and dynamic relationships they establish with various hosts and environmental niches. Notably, fungi are integral to disease processes and a wide array of biotechnological innovations, highlighting their significance in medical, agricultural, and industrial domains. Recent advances in genetic engineering have revolutionized fungal research, with CRISPR/Cas emerging as the most potent and versatile genome editing platform. This technology enables precise manipulation of fungal genomes, from silencing efflux pump genes in Candida albicans (enhancing antifungal susceptibility) to targeting virulence-associated sirtuins in Aspergillus fumigatus (attenuating pathogenicity). Its applications span gene overexpression, multiplexed mutagenesis, and secondary metabolite induction, proving transformative for disease management and biotechnological innovation. CRISPR/Cas9's advantages-unmatched precision, cost-effectiveness, and therapeutic potential-are tempered by challenges like off-target effects, ethical dilemmas, and regulatory gaps. Integrating nanoparticle delivery systems and multi-omics approaches may overcome technical barriers, but responsible innovation requires addressing these limitations. CRISPR-driven fungal genome editing promises to redefine solutions for drug-resistant infections, sustainable bioproduction, and beyond as the field evolves. In conclusion, genome editing technologies have enhanced our capacity to dissect fungal biology and expanded fungi's practical applications across various scientific and industrial domains. Continued innovation in this field promises to unlock the vast potential of fungal systems further, enabling more profound understanding and transformative biotechnological progress.

Bio-induced overproduction of heterocycloanthracin-like bacteriocin in Lysinibacillus macroides by Aspergillus austroafricanus: optimization of medium conditions and evaluation of potential applications

BACKGROUND

Plants and microorganisms are at the forefront of natural exploitable bioresources for the discovery of novel bioactive compounds (BACs) to provide solutions to food and agricultural challenges. The present study aimed to produce a novel biotechnologically-relevant BAC from a mangrove sediment bacterium under optimized bioprocess medium conditions. The BAC-producing bacteria were isolated via the crowded plate technique, and medium optimization was performed via sequential statistics of response surface methodology (RSM). The RSM model predictions were optimized, validated, and scaled up in a 5-L bioreactor via submerged batch fermentation. The BAC was extracted with ethyl acetate, purified via silica gel column chromatography, and identified via semipreparative high-performance liquid chromatography using bioactive standards with known retention times. The biocontrol, antioxidant and biopreservation potential of the BAC were evaluated via standard methods.

RESULTS

The results revealed that strain GKRMS-A9 produced the largest inhibition zone diameter (ZND) of 17 mm against the susceptible mould. The bacterium and its susceptible mould were identified as Lysinibacillus macroides and Aspergillus austroafricanus strains, respectively. Bioprocess medium optimization produced 9.6 g L- 1 of the BAC with a ZND of 47.1 mm using 44.84% [v v- 1] rice processing effluent, 8.58 gL- 1 casamino acid, 1.39 g L- 1 MgSO4.7H2O, 2.78 g L- 1 CaCl2.2H2O, 16.94% [v v- 1] inoculum volume, and 10.45 g L- 1 Na2HPO4/NaH2PO4. The BAC concentration increased 48.7-fold in response to biological induction with susceptible mould. Silica gel chromatography revealed 9 bioactive fractions in the ethyl acetate extract, with fraction C (retention time of 9.02 min) eliciting the largest mean ZND of 38.1 ± 1.7 mm against Aspergillus austroafricanus. Fraction C was identified as a heterocycloanthracin-like class II bacteriocin with a molecular weight of 10.5 kDa.

CONCLUSION

The bacteriocin 'macroidin' is stable over a wide range of pH values and temperatures and has significant antimicrobial activity against Gram-positive food-borne and phytopathogenic strains of bacteria and moulds. Its antioxidant activities against DPPH and ABTS*+ radicals are comparable to those of ascorbic acid, making this biomolecule a promising agent for biopreservation and phytopathogen control applications in the food and agricultural sectors.

Recent advances in yeast and bacteria co-cultivation for bioprocess applications

Yeast and bacteria co-cultures can be found in nature and have multiple advantages that can be exploited, nowadays also in a controlled bioproduction environment. Various types of co-cultivation have been used for food applications such as production of flavor compounds in dairy products and alcoholic beverages. Co-cultures can broaden the substrate spectrum for microbial food and feed production, they can increase productivity and efficiency, and the nutritional value. Workflows have been developed from plate to bioreactor scale to increase reproducibility and optimize benefits of individual co-cultivation strategies. Nonetheless, certain limitations need to be overcome for industrial application. Many interactions of microbes, in particular in suspension cultures, are not sufficiently understood or even explored. While more possibilities arose from on-line monitoring of individual populations or even single cells, off-line measurement techniques are still typically applied in order to assess growth and product formation. Promising advances have been achieved, however, by methods for single-cell at-line and on-line analysis in co-cultures which are accounted for to emphasize the current opportunities and challenges in monitoring and controlling co-cultures. This review aims to summarize the recent advances with a particular focus on cultivation procedures and process analysis in bacteria, yeast and bacteria-yeast co-cultures. The implementation of suitable monitoring methods to enable (remote) control and contribute to quality assurance will accelerate the development and optimization of industrial co-culture bioprocesses. This will support transferability and process standardization across world regions adding to the advancement of bioproduction. The applicability of some relevant technology is, however, in its infancy.

Strategies for Actinobacteria Isolation, Cultivation, and Metabolite Production that Are Biologically Important

Novel antimicrobial agents are urgently needed to combat antimicrobial resistance from multidrug-resistant organisms. Actinobacteria are key sources of bioactive metabolites with diverse biological activities. Despite their contributions to drug discovery, the process from strain identification to drug manufacturing faces many challenges, especially the rediscovery of known compounds. Recent technological and scientific advancements have accelerated drug development. Efforts to isolate and screen rare actinobacterial species could yield novel bioactive compounds. This review summarizes techniques for selectively isolating rare actinobacteria, improving bioactive metabolite production, and discovering potential strains. Notably, new genomic strategies and new discoveries regarding spectroscopic signature-based bioactive natural products containing specific structural motifs are also discussed. Furthermore, this review updates the compounds derived from rare actinobacteria and their biological applications.

Effects of Magnaporthe oryzae cell-free filtrate on the secondary metabolism of Streptomyces bikiniensis HD-087: a non-targeted metabolomics analysis

Rice blast, a disease caused by Magnaporthe oryzae, significantly threatens global rice production. To improve the anti-M. oryzae activity of Streptomyces bikiniensis HD-087 metabolites, the effects of inducer, Magnaporthe oryzae acellular filtrate, on secondary metabolism of S. bikiniensis HD-087 were studied. The results showed that M. oryzae cell-free filtrate cultured for 96 h served as the most effective inducer, significantly enhancing the anti-M. oryzae activity of metabolites of S. bikiniensis HD-087 and increasing the diameter of the inhibitory zone by 2.96 mm. The inhibition rates of M. oryzae colony diameter and spore germination in the induced group were 12.39% and 39.6% higher than those in the non-induced group, respectively. Metabolomic profiling of strain HD-087 highlighted substantial differences between the induced and non-induced groups. At 48 h of fermentation, a total of 705 distinct metabolites were identified, while at 96 h this number decreased to 321. Moreover, induction markedly altered primary pathways such as the tricarboxylic acid cycle, amino acid biosynthesis, and fatty acid metabolism in S. bikiniensis HD-087. qPCR analysis showed that nrps genes and pks genes in the induced group were significantly up-regulated by 9.92 ± 0.51 and 2.71 ± 0.17 times, respectively, and biotin carboxylase activity was also increased 26.63%. These results provide a theoretical basis for using inducers to enhance the antimicrobial ability of Streptomyces.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Marine natural product-inspired discovery of novel BRD4 inhibitors with anti-inflammatory activity

Bromodomain-containing protein 4 (BRD4) has been identified as a promising target in drug discovery, and the development of novel specific BRD4 bromodomain inhibitors will benefit anti-inflammatory drug discovery as well as bromodomain function role disclose. Herein, inspired by marine quinazolinone alkaloid penipanoid C, we designed and synthesized a series of quinazolin-4(3H)-ones with diverse linkers between two aromatic ring systems. Among them, compound 25 possessed good in vitro BRD4 inhibitory activities (IC50 = 3.64 μM for BRD4 BD1 and IC50 = 0.12 μM for BRD4 BD2) and anti-inflammatory activity (IC50 = 1.98 μM for NO production assay). Meantime, 25 obviously suppressed the expression of TNF-α and IL-6 in LPS-stimulated Raw 264.7 and THP-1 cells. Notablely, 25 displayed in vivo therapeutic efficacies in an acute inflammation model without obvious cytotoxicity. These findings suggest that 25 is a selective BRD4 BD2 inhibitor which is a promising anti-inflammatory lead compound worthy for further investigation.

Quinazolinone Derivative MR2938 Protects DSS-Induced Barrier Dysfunction in Mice Through Regulating Gut Microbiota

Background/Objectives: Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by colorectal immune infiltration and significant microbiota compositional changes. Gut microbiota homeostasis is necessary to maintain the healthy state of humans. MR2938, a quinazolin-4(3H)-one derivative derived from the marine natural product penipanoid C, alleviated DSS-induced colitis in a dose-dependent manner. Herein, we aimed to investigate the impact of MR2938 on the gut microbiota in dextran sodium sulfate (DSS)-induced colitis in mice and to elucidate the role of the gut microbiota in the therapeutic mechanism of MR2938 for alleviating colitis. Methods: Acute colitis was induced with DSS in mice. Mice were administered with 100 mg/kg or 50 mg/kg of MR2938. Cecal content was also preserved in liquid nitrogen and subsequently analyzed following 16S RNA sequencing. Antibiotic cocktail-induced microbiome depletion was performed to further investigate the relationship between MR2938 and gut microbiota. The inflammatory factor levels were performed by quantitative polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA). Alcian blue staining and immunofluorescence were used to estimate the intestinal barrier. Results: The 16S rRNA sequencing revealed microbiota modulation by MR2938. Compared with the model group, the 100 mg/kg MR2938 group was associated with higher abundances of Entercoccus and a lower abundance of Staphylococcus, while the 50 mg/kg MR2938 group was associated with higher abundances of Lactobacillus and a lower abundance of Staphylococcus. The antibiotic-mediated microbiota depletion experiments demonstrated that the gut microbiota primarily contributed to barrier function protection, with little impact on inflammatory factor levels during the MR2938 treatment. Conclusions: These findings suggest that intestinal flora play a crucial role in MR2938's therapeutic mechanism for alleviating colitis.

The efficient green bio-manufacturing of Vitamin K2: design, production and applications

Vitamin K2, also known as methylnaphthoquinone, is a crucial fat-soluble nutrient necessary for the human body. The biological production of Vitamin K2 has received widespread attention due to its environmental friendliness and maneuverability in recent years. This review provides insights into the modular metabolic pathways of Vitamin K2, lays the foundation for microbial metabolic flow balancing, cofactor engineering and dynamic regulation, and realizes the production of Vitamin K2 by synthesizing artificial cells from scratch. With the intensive development of modern fermentation technology, methods for the preparation of Vitamin K2 using the fermentation strategies of co-culturing and biofilm reactors have emerged. In prokaryotes, the introduction of heptenyl pyrophosphate synthase (HepPPS) and mevalonate acid (MVA) pathway solved the problem of insufficient precursors for Vitamin K2 production but still did not meet the market demand. Therefore, enhancing expression through multi-combinatorial metabolic regulation and innovative membrane reactors is an entry point for future research. Due to the light-induced decomposition and water-insoluble nature of Vitamin K2, the secretion regulation and purification processing also need to be considered in the actual production. Also, it summarizes the research progress of Vitamin K2 in the food and pharmaceutical fields. Additionally, the future development trend and application prospect of Vitamin K2 are also discussed to provide guidance for Vitamin K2 biosynthesis and application.

Profiling of bioactive secondary metabolites from Aspergillus niger against a guava wilt pathogen, Fusarium oxysporum f. sp. psidii

Guava wilt is a devastating soil-borne disease that causes significant losses in guava orchards. Management of the disease is very challenging once established in the field. Therefore, there is a need to explore for an effective, economical, and sustainable management strategies. Aspergillus niger, a bio-control fungus, has been demonstrated effectiveness against various soil-borne pathogens including guava wilt pathogens. It produces a diverse hydrolysing enzymes and secondary metabolites. However, no extensive study has been undertaken to profile the secondary metabolites of A. niger. In this investigation, we assessed eleven A. niger strains (AN-1 to AN-11) against four guava wilt pathogens (Fusarium oxysporum f. sp. psidii, F. falciforme, F. chlamydosporum, and F. verticillioides) using a dual culture assay. All strains demonstrated effective by restricting the mycelial growth of pathogens, among them AN-11 displayed maximum inhibition of 86.33%, followed by the AN-3 (84.27%). The UPLC-QToF-ESIMS analysis was undertaken to explore the secondary metabolites of AN-11 responsible for inhibiting F. oxysporum f. sp. psidii. The crude extracts were obtained from F. oxysporum f. sp. psidii, AN-11 and their interaction using ethyl acetate as a solvent. After evaporating, the crude fractions were analysed using UPLC-QToF-ESIMS with an Acquity UPLC and a SCIEX SelexION Triple QuadTM 5500 System. From the ethyl acetate extract of F. oxysporum f. sp. psidii, approximately 14 metabolites involved in pathogenicity were identified. Similarly, analysis of AN-11 crude extract revealed 25 metabolites, and notably, 41 metabolites were identified during the interaction between AN-11 and F. oxysporum f. sp. psidii, including kotanin, isokotanin A, aurofusarin, kojic acid, pyranonigrin, aurasperone F, hexylitaconic acid, asperazine, bicoumanigrin, chloramphenicol, cephalosporin C, fusarin C, zearalonone, fonsecin B, malformin A, and others. Among these, 21 metabolites were produced only during the interaction and have antimicrobial properties. This study highlights the significant potential of the AN-11 strain in generating a diverse array of non-volatile secondary metabolites with antimicrobial properties. These metabolites could be further extracted and investigated for their efficacy against other soil borne pathogens and potentially developed into formulations for controlling plant diseases.

Volatile Organic Compounds Produced by Co-Culture of Burkholderia vietnamiensis B418 with Trichoderma harzianum T11-W Exhibits Improved Antagonistic Activities against Fungal Phytopathogens

Recently, there has been a growing interest in the biocontrol activity of volatile organic compounds (VOCs) produced by microorganisms. This study specifically focuses on the effects of VOCs produced by the co-culture of Burkholderia vietnamiensis B418 and Trichoderma harzianum T11-W for the control of two phytopathogenic fungi, Botrytis cinerea and Fusarium oxysporum f. sp. cucumerium Owen. The antagonistic activity of VOCs released in mono- and co-culture modes was evaluated by inhibition assays on a Petri dish and in detached fruit experiments, with the co-culture demonstrating significantly higher inhibitory effects on the phytopathogens on both the plates and fruits compared with the mono-cultures. Metabolomic profiles of VOCs were conducted using the solid-liquid microextraction technique, revealing 341 compounds with significant changes in their production during the co-culture. Among these compounds, linalool, dimethyl trisulfide, dimethyl disulfide, geranylacetone, 2-phenylethanol, and acetophenone were identified as having strong antagonistic activity through a standard inhibition assay. These key compounds were found to be related to the improved inhibitory effect of the B418 and T11-W co-culture. Overall, the results suggest that VOCs produced by the co-culture of B. vietnamiensis B418 and T. harzianum T11-W possess great potential in biological control.

Identification and characterization of the siderochelin biosynthetic gene cluster via coculture

Many microbial biosynthetic gene clusters (BGCs) are inactive under standard laboratory conditions, making characterization of their products difficult. Silent BGCs are likely activated by specific cues in their natural environment, such as the presence of competitors. Growth conditions such as coculture with other microbes, which more closely mimic natural environments, are practical strategies for inducing silent BGCs. Here, we utilize coculture to activate BGCs in nine actinobacteria strains. We observed increased production of the ferrous siderophores siderochelin A and B during coculture of Amycolatopsis strain WAC04611 and Tsukamurella strain WAC06889b. Furthermore, we identified the siderochelin BGC in WAC04611 and discovered that the GntR-family transcription factor sidR3 represses siderochelin production. Deletion of the predicted aminotransferase sidA abolished production of the carboxamides siderochelin A/B and led to the accumulation of the carboxylate siderochelin D. Finally, we deleted the predicted hydroxylase sidB and established that it is essential for siderochelin production. Our findings show that microbial coculture can successfully activate silent BGCs and lead to the discovery and characterization of unknown BGCs for molecules like siderochelin.IMPORTANCESiderophores are vital iron-acquisition elements required by microbes for survival in a variety of environments. Furthermore, many siderophores are essential for the virulence of various human pathogens, making them a possible target for antibacterials. The significance of our work is in the identification and characterization of the previously unknown BGC for the siderophore siderochelin. Our work adds to the growing knowledge of siderophore biosynthesis, which may aid in the future development of siderophore-targeting pharmaceuticals and inform on the ecological roles of these compounds. Furthermore, our work demonstrates that combining microbial coculture with metabolomics is a valuable strategy for identifying upregulated compounds and their BGCs.

Pleiotropically activation of azaphilone biosynthesis by overexpressing a pathway-specific transcription factor in marine-derived Aspergillus terreus RA2905

The genome sequencing of Aspergillus terreus reveals that the vast number of predicted biosynthetic gene clusters have not reflected by the metabolic profile observed under conventional culture conditions. In this study, a silent azaphilone biosynthetic gene cluster was activated by overexpressing a pathway-specific transcription factor gene2642 in marine-derived fungus A. terreus RA2905. Consequently, twenty azaphilone compounds were identified from the OE2642 mutant, including 11 new azaphilones and their precursors, azasperones C-J (1-5, 7-9) and preazasperones A-C (15-17). The structures of those new compounds were unambiguously determined on the basis of NMR and HRESIMS spectra analysis, and the absolute configurations were established depending on ECD calculations. Compounds 1 and 2 were the rarely reported naturally occurring azaphilones with 2-N coupled phenyl-derivative. The bioactivity assay revealed that compounds 18-20 exhibited significant anti-inflammatory activity. Based on the occurrence of diverse intermediates and the putative gene functions, a plausible biosynthetic pathway of these compounds was proposed. The above results demonstrated that overexpression of the pathway-specific transcription factor presents a promising approach for enriching fungal secondary metabolites and accelerating the targeted discovery of novel biosynthetic products.

Synergistic Biocontrol and Growth Promotion in Strawberries by Co-Cultured Trichoderma harzianum TW21990 and Burkholderia vietnamiensis B418

This study aimed to investigate the efficiency of the secondary metabolites (SMs) produced by a co-culture of Trichoderma harzianum TW21990 and Burkholderia vietnamiensis B418 in the control of Colletotrichum siamense CM9. A fermentation filtrate of B418 + TW21990 co-culture (BT21) produced a notable increase in the inhibition rate of CM9 compared to those of TW21990 and B418 monocultures, which reached 91.40% and 80.46% on PDA plates and strawberry leaves, respectively. The BT21 fermentation broth exhibited high control efficiency on strawberry root rot of 68.95% in a pot experiment, which was higher than that in the monocultures and fluazinam treatment. In addition, BT21 treatment promoted strawberry root development, improved antioxidative enzyme activities in the leaves and roots, and enhanced the total chlorophyll content of the strawberry leaves. UHPLC-MS/MS analysis of fermentation filtrates was performed to elucidate SM variations, revealing 478 and 795 metabolites in BT21 co-culture in positive and negative ion modes, respectively. The metabolomic profiles suggested abundant SMs with antagonistic capabilities and growth-promoting effects: 3-(propan-2-yl)-octahydropyrrolo [1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Val)), 3-[(4-hydroxyphenyl)methyl]-octahydropyrrolo[1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Tyr)), 3-indoleacetic acid (IAA), 2-hydroxycinnamic acid, 4-aminobutyric acid (GABA), bafilomycin B1, and DL-indole-3-lactic acid (ILA) were significantly enhanced in the co-culture. Overall, this study demonstrates that a co-culture strategy is efficient for inducing bioactive SMs in T. harzianum and B. vietnamiensis, which could be exploited as a novel approach for developing biocontrol consortia.

The repertoire and levels of secondary metabolites in microbial cocultures depend on the inoculation ratio: a case study involving Aspergillus terreus and Streptomyces rimosus

OBJECTIVE

The aim of this study was to determine the influence of the inoculation volume ratio on the production of secondary metabolites in submerged cocultures of Aspergillus terreus and Streptomyces rimosus.

RESULTS

The shake flask cocultures were initiated by using 23 inoculum variants that included different volumes of A. terreus and S. rimosus precultures. In addition, the axenic controls were propagated in parallel with the cocultures. UPLC‒MS analysis revealed the presence of 15 secondary metabolites, 12 of which were found both in the "A. terreus vs. S. rimosus" cocultures and axenic cultures of either A. terreus or S. rimosus. The production of the remaining 3 molecules was recorded solely in the cocultures. The repertoire and quantity of secondary metabolites were evidently dependent on the inoculation ratio. It was also noted that detecting filamentous structures resembling typical morphological forms of a given species was insufficient to predict the presence of a given metabolite.

CONCLUSIONS

The modification of the inoculation ratio is an effective strategy for awakening and enhancing the production of secondary metabolites that are not biosynthesized under axenic conditions.

Strategies to enhance production of metabolites in microbial co-culture systems

Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.

Unlocking fungal quorum sensing: Oxylipins and yeast interactions enhance secondary metabolism in monascus

Exploring the symbiotic potential between fungal and yeast species, this study investigates the co-cultivation dynamics of Monascus, a prolific producer of pharmacologically relevant secondary metabolites, and Wickerhamomyce anomalous. The collaborative interaction between these microorganisms catalyzed a substantial elevation in the biosynthesis of secondary metabolites, prominently Monacolin K and natural pigments. Central to our discoveries was the identification and enhanced production of oxylipins (13S-hydroxyoctadecadienoic acid，13S-HODE), putative quorum-sensing molecules, within the co-culture environment. Augmentation with exogenous oxylipins not only boosted Monacolin K production by over half but also mirrored morphological adaptations in Monascus, affecting both spores and mycelial structures. This augmentation was paralleled by a significant upregulation in the transcriptional activity of genes integral to the Monacolin K biosynthetic pathway, as well as genes implicated in pigment and spore formation. Through elucidating the interconnected roles of quorum sensing, G-protein-coupled receptors, and the G-protein-mediate signaling pathway, this study provides a comprehensive view of the molecular underpinnings facilitating these metabolic enhancements. Collectively, our findings illuminate the profound influence of Wickerhamomyces anomalous co-culture on Monascus purpureus, advocating for oxylipins as a pivotal quorum-sensing mechanism driving the observed symbiotic benefits.

The limitless endophytes: their role as antifungal agents against top priority pathogens

Multi resistant fungi are on the rise, and our arsenal compounds are limited to few choices in the market such as polyenes, pyrimidine analogs, azoles, allylamines, and echinocandins. Although each of these drugs featured a unique mechanism, antifungal resistant strains did emerge and continued to arise against them worldwide. Moreover, the genetic variation between fungi and their host humans is small, which leads to significant challenges in new antifungal drug discovery. Endophytes are still an underexplored source of bioactive secondary metabolites. Many studies were conducted to isolate and screen endophytic pure compounds with efficacy against resistant yeasts and fungi; especially, Candida albicans, C. auris, Cryptococcus neoformans and Aspergillus fumigatus, which encouraged writing this review to critically analyze the chemical nature, potency, and fungal source of the isolated endophytic compounds as well as their novelty features and SAR when possible. Herein, we report a comprehensive list of around 320 assayed antifungal compounds against Candida albicans, C. auris, Cryptococcus neoformans and Aspergillus fumigatus in the period 1980-2024, the majority of which were isolated from fungi of orders Eurotiales and Hypocreales associated with terrestrial plants, probably due to the ease of laboratory cultivation of these strains. 46% of the reviewed compounds were active against C. albicans, 23% against C. neoformans, 29% against A. fumigatus and only 2% against C. auris. Coculturing was proved to be an effective technique to induce cryptic metabolites absent in other axenic cultures or host extract cultures, with Irperide as the most promising compounds MIC value 1 μg/mL. C. auris was susceptible to only persephacin and rubiginosin C. The latter showed potent inhibition against this recalcitrant strain in a non-fungicide way, which unveils the potential of fungal biofilm inhibition. Further development of culturing techniques and activation of silent metabolic pathways would be favorable to inspire the search for novel bioactive antifungals.

Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach

In their natural habitats, microbes rarely exist in isolation; instead, they thrive in consortia, where various interactions occur. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which supplies sucrose to the heterotrophic P. putida cscRABY, is investigated to identify potential interactions. Initial experiments reveal a remarkable growth-promoting effect of the heterotrophic partner on the cyanobacterium, resulting in an up to 80% increase in the growth rate and enhanced photosynthetic capacity. Vice versa, the presence of the cyanobacterium has a neutral effect on P. putida cscRABY, highlighting the resilience of pseudomonads against stress and their potential as co-culture partners. Next, a suitable reference process reinforcing the growth-promoting effect is established in a parallel photobioreactor system, which sets the basis for the analysis of the co-culture at the transcriptome, proteome, and metabolome levels. In addition to several moderate changes, including alterations in the metabolism and stress response in both microbes, this comprehensive multi-OMICs approach strongly hints towards the exchange of further molecules beyond the unidirectional feeding with sucrose. Taken together, these findings provide valuable insights into the complex dynamics between both co-culture partners, indicating multi-level interactions, which can be employed for further streamlining of the co-cultivation system.

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria

Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.

Secondary Metabolites from Fungi Microsphaeropsis spp.: Chemistry and Bioactivities

Microsphaeropsis, taxonomically classified within the kingdom fungi, phylum Ascomycota, subphylum Deuteromycotina, class Coelomycetes, order Sphaeropsidales, and family Sphaeropsidaceae, exhibit a ubiquitous distribution across various geographical regions. These fungi are known for their production of secondary metabolites, characterized by both structural novelty and potent biological activity. Consequently, they represent a significant reservoir for the advancement of novel pharmaceuticals. In this paper, a systematic review was present, marking the analysis of secondary metabolites synthesized by Microsphaeropsis reported between 1980 and 2023. A total of 112 compounds, comprising polyketones, macrolides, terpenoids, and nitrogen-containing compounds, were reported from Microsphaeropsis. Remarkably, among these compounds, 49 are novel discoveries, marking a significant contribution to the field. A concise summary of their diverse biological activities was provided, including antibacterial, antitumor, and antiviral properties and other bioactivities. This analysis stands as a valuable reference, poised to guide further investigations into the active natural products derived from Microsphaeropsis and their potential contributions to the development of medicinal resources.

Interplay of emerging and established technologies drives innovation in natural product antibiotic discovery

A continued rise of antibiotic resistance and shortages of effective antibiotics necessitate the discovery and development of new antibiotics with novel modes of action (MoAs) against resistant pathogens. While natural products remain the best resource for antibiotic discovery, their exploration faces many challenges, including (i) unknown MoAs, (ii) high rediscovery rates, (iii) tedious isolation and structure elucidation, and (iv) insufficient production for further development. We have identified recent innovations in screening methods, microbiology, bioinformatics, and metabolomics technologies, as well as natural product-inspired synthesis and synthetic biology, that have contributed to new natural product antibiotics in the past two years. We highlight their interplay as the key element for successful applications, driving future opportunities to increase the pool of natural product-based antibacterial antibiotics.

Exploring Diverse Bioactive Secondary Metabolites from Marine Microorganisms Using Co-Culture Strategy

The isolation and identification of an increasing number of secondary metabolites featuring unique skeletons and possessing diverse bioactivities sourced from marine microorganisms have garnered the interest of numerous natural product chemists. There has been a growing emphasis on how to cultivate microorganisms to enhance the chemical diversity of metabolites and avoid the rediscovery of known ones. Given the significance of secondary metabolites as a means of communication among microorganisms, microbial co-culture has been introduced. By mimicking the growth patterns of microbial communities in their natural habitats, the co-culture strategy is anticipated to stimulate biosynthetic gene clusters that remain dormant under traditional laboratory culture conditions, thereby inducing the production of novel secondary metabolites. Different from previous reviews mainly focusing on fermentation conditions or metabolite diversities from marine-derived co-paired strains, this review covers the marine-derived co-culture microorganisms from 2012 to 2022, and turns to a particular discussion highlighting the selection of co-paired strains for marine-derived microorganisms, especially the fermentation methods for their co-cultural apparatus, and the screening approaches for the convenient and rapid detection of novel metabolites, as these are important in the co-culture. Finally, the structural and bioactivity diversities of molecules are also discussed. The challenges and prospects of co-culture are discussed on behave of the views of the authors.

Effects of the Coculture Initiation Method on the Production of Secondary Metabolites in Bioreactor Cocultures of Penicillium rubens and Streptomyces rimosus

Bioreactor cocultures involving Penicillium rubens and Streptomyces rimosus were investigated with regard to secondary metabolite production, morphological development, dissolved oxygen levels, and carbon substrate utilization. The production profiles of 22 secondary metabolites were analyzed, including penicillin G and oxytetracycline. Three inoculation approaches were tested, i.e., the simultaneous inoculation of P. rubens with S. rimosus and the inoculation of S. rimosus delayed by 24 or 48 h relative to P. rubens. The delayed inoculation of S. rimosus into the P. rubens culture did not prevent the actinomycete from proliferating and displaying its biosynthetic repertoire. Although a period of prolonged adaptation was needed, S. rimosus exhibited growth and the production of secondary metabolites regardless of the chosen delay period (24 or 48 h). This promising method of coculture initiation resulted in increased levels of metabolites tentatively identified as rimocidin B, 2-methylthio-cis-zeatin, chrysogine, benzylpenicilloic acid, and preaustinoid D relative to the values recorded for the monocultures. This study demonstrates the usefulness of the delayed inoculation approach in uncovering the metabolic landscape of filamentous microorganisms and altering the levels of secondary metabolites.

Bioactive compounds and biomedical applications of endophytic fungi: a recent review

Human life has been significantly impacted by the creation and spread of novel species of antibiotic-resistant bacteria and virus strains that are difficult to manage. Scientists and researchers have recently been motivated to seek out alternatives and other sources of safe and ecologically friendly active chemicals that have a powerful and effective effect against a wide variety of pathogenic bacteria as a result of all these hazards and problems. In this review, endophytic fungi and their bioactive compounds and biomedical applications were discussed. Endophytes, a new category of microbial source that can produce a variety of biological components, have major values for study and broad prospects for development. Recently, endophytic fungi have received much attention as a source for new bioactive compounds. In addition, the variety of natural active compounds generated by endophytes is due to the close biological relationship between endophytes and their host plants. The bioactive compounds separated from endophytes are usually classified as steroids, xanthones, terpenoids, isocoumarins, phenols, tetralones, benzopyranones and enniatines. Moreover, this review discusses enhancement methods of secondary metabolites production by fungal endophytes which include optimization methods, co-culture method, chemical epigenetic modification and molecular-based approaches. Furthermore, this review deals with different medical applications of bioactive compounds such as antimicrobial, antiviral, antioxidant and anticancer activities in the last 3 years.

Modern Trends in Natural Antibiotic Discovery

Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.

Elevated antimony concentration stimulates rare taxa of potential autotrophic bacteria in the Xikuangshan groundwater

Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along an Sb concentration gradient in the Xikuangshan antimony mine area and subjected to high through-put sequencing of 16S rRNA genes to investigate the bacterial communities. Results suggested that both abundant and rare sub-communities were dominated by Betaproteobacteria, Gammaproteobacteria, and Alphaproteobacteria, whereas rare sub-communities showed higher alpha-diversities. Multivariate analysis showed that both the abundant and rare taxa were under the stress of Sb, but the impact on rare taxa was greater. Nitrate explained a large part for the variation of the abundant sub-communities, indicating the critical role of nitrate for their activities under anoxic conditions. In contrast, bicarbonate significantly impacted rare sub-communities, suggesting their potential autotrophic characteristics. To further explore the role of rare taxa in the communities and the mechanism of affecting the community composition, a network was constructed to display the co-occurrence pattern of bacterial communities. The rare taxa contributed most of the network nodes and served as keystone species to maintain the stability of community. Abiotic factors (mainly Sb and pH) and bacterial interspecific interactions (interactions between keystone species and other bacterial groups) jointly affect the community dynamics. Functional prediction was performed to further reveal the ecological function of rare taxa in the Sb-disturbed groundwater environment. The results indicated that the rare taxa harbored much more diverse functions than their abundant counterparts. Notably, elevated Sb concentration promoted some potential autotrophic functions in rare taxa such as the oxidation of S-, N-, and Fe(II)-compounds. These results offer new insights into the roles of rare species in elemental cycles in the Sb-impacted groundwater.

Exploring the Impact of Tensions in Stakeholder Norms on Designing for Value Change: The Case of Biosafety in Industrial Biotechnology

Synthetic biologists design and engineer organisms for a better and more sustainable future. While the manifold prospects are encouraging, concerns about the uncertain risks of genome editing affect public opinion as well as local regulations. As a consequence, biosafety and associated concepts, such as the Safe-by-design framework and genetic safeguard technologies, have gained notoriety and occupy a central position in the conversation about genetically modified organisms. Yet, as regulatory interest and academic research in genetic safeguard technologies advance, the implementation in industrial biotechnology, a sector that is already employing engineered microorganisms, lags behind. The main goal of this work is to explore the utilization of genetic safeguard technologies for designing biosafety in industrial biotechnology. Based on our results, we posit that biosafety is a case of a changing value, by means of further specification of how to realize biosafety. Our investigation is inspired by the Value Sensitive Design framework, to investigate scientific and technological choices in their appropriate social context. Our findings discuss stakeholder norms for biosafety, reasonings about genetic safeguards, and how these impact the practice of designing for biosafety. We show that tensions between stakeholders occur at the level of norms, and that prior stakeholder alignment is crucial for value specification to happen in practice. Finally, we elaborate in different reasonings about genetic safeguards for biosafety and conclude that, in absence of a common multi-stakeholder effort, the differences in informal biosafety norms and the disparity in biosafety thinking could end up leading to design requirements for compliance instead of for safety.

Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises

Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.

Marine natural products

Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.

Identification of marine natural product Pretrichodermamide B as a STAT3 inhibitor for efficient anticancer therapy

The Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) regulates the expression of various critical mediators of cancer and is considered as one of the central communication nodes in cell growth and survival. Marine natural products (MNP) represent great resources for discovery of bioactive lead compounds, especially anti-cancer agents. Through the medium-throughput screening of our in-house MNP library, Pretrichodermamide B, an epidithiodiketopiperazine, was identified as a JAK/STAT3 signaling inhibitor. Further studies identified that Pretrichodermamide B directly binds to STAT3, preventing phosphorylation and thus inhibiting JAK/STAT3 signaling. Moreover, it suppressed cancer cell growth, in vitro, at low micromolar concentrations and demonstrated efficacy in vivo by decreasing tumor growth in a xenograft mouse model. In addition, it was shown that Pretrichodermamide B was able to induce cell cycle arrest and promote cell apoptosis. This study demonstrated that Pretrichodermamide B is a novel STAT3 inhibitor, which should be considered for further exploration as a promising anti-cancer therapy.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00162-x.

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.

Bioactive Alpha-Pyrone and Phenolic Glucosides from the Marine-Derived Metarhizium sp. P2100

Glycoside compounds have attracted great interest due to their remarkable and multifarious bioactivities. In this study, four hitherto unknown 4-methoxy-β-D-glucosyl derivatives were obtained and identified from the marine-derived fungus Metarhizium sp. P2100, including three alpha-pyrone glycosides (1-3) and one phenolic glycoside (4). Their planar structures were elucidated by comprehensive spectroscopic analysis, including 1D/2D NMR and HRESIMS. The absolute configurations of 1-3 were determined by a single-crystal X-ray crystallographic experiment, a comparison of the experimental, and a calculated electronic circular dichroism (ECD) spectra, respectively. Compounds 2 and 3 are a pair of rare epimeric pyranoside glycosides at C-7 with a core of aglycone as 2H-pyrone. Compounds 1-4 exhibited weak anti-inflammatory activities. In particular, compounds 1-3 displayed inhibitory activities against α-amylase, showing a potential for the development of a new α-amylase inhibitor for controlling diabetes.

Bioactive Alkaloids from the Marine-Derived Fungus Metarhizium sp. P2100

The Metarhizium fungal species are considered the prolific producers of bioactive secondary metabolites with a variety of chemical structures. In this study, the biosynthetic potential of marine-derived fungus Metarhizium sp. P2100 to produce bioactive alkaloids was explored by using the one strain many compounds (OSMAC) strategy. From the rice solid medium (mixed with glucose peptone and yeast broth (GPY)), wheat solid medium (mixed with Czapek) and GPY liquid medium, one rare N-butenone spiroquinazoline alkaloid, N-butenonelapatin A (1), together with nine known compounds (2-10), were isolated and identified. Their structures were elucidated by analysis of the comprehensive spectroscopic data, including 1D and 2D NMR and HRESIMS, and the absolute configuration of 1 was determined by a single-crystal X-ray crystallographic experiment. N-butenonelapatin A (1) represents the first example of N-butenone spiroquinazoline with a rare α, β-unsaturated ketone side chain in the family of spiroquinazoline alkaloids. Compound 4 displayed antibacterial activity against Vibrio vulnificus MCCC E1758 with a minimum inhibitory concentration (MIC) value of 6.25 µg/mL. Compound 7 exhibited antibacterial activities against three aquatic pathogenic bacteria, including V. vulnificus MCCC E1758, V. rotiferianus MCCC E385 and V. campbellii MCCC E333 with the MIC values of 12.5, 12.5 and 6.25 μg/mL, respectively. Compounds 3 and 6 demonstrated anti-inflammatory activity against NO production induced by lipopolysaccharide (LPS) with the IC50 values of 37.08 and 37.48 μM, respectively. In addition, compound 1 showed weak inhibitory activity against the proliferation of tumor cell lines A-375 and HCT 116. These findings further demonstrated that fungi of the Metarhizium species harbor great potentials in the synthesis of a variety of bioactive alkaloids.

Induction of Secondary Metabolite Biosynthesis by Deleting the Histone Deacetylase HdaA in the Marine-Derived Fungus Aspergillus terreus RA2905

Aspergillus terreus is well-known for its ability to biosynthesize valuable pharmaceuticals as well as structurally unique secondary metabolites. However, numerous promising cryptic secondary metabolites in this strain regulated by silent gene clusters remain unidentified. In this study, to further explore the secondary metabolite potential of A. terreus, the essential histone deacetylase hdaA gene was deleted in the marine-derived A. terreus RA2905. The results showed that HdaA plays a vital and negative regulatory role in both conidiation and secondary metabolism. Loss of HdaA in A. terreus RA2905 not only resulted in the improvement in butyrolactone production, but also activated the biosynthesis of new azaphilone derivatives. After scaled fermentation, two new azaphilones, asperterilones A and B (1 and 2), were isolated from ΔhdaA mutant. The planar structures of compounds 1 and 2 were undoubtedly characterized by NMR spectroscopy and mass spectrometry analysis. Their absolute configurations were assigned by circular dichroism spectra analysis and proposed biosynthesis pathway. Compounds 1 and 2 displayed moderate anti-Candida activities with the MIC values ranging from 18.0 to 47.9 μM, and compound 1 exhibited significant cytotoxic activity against human breast cancer cell line MDA-MB-231. This study provides novel evidence that hdaA plays essential and global roles in repressing secondary metabolite gene expression in fungi, and its deletion represents an efficient strategy to mine new compounds from A. terreus and other available marine-derived fungi.

Chemical and biological diversity of new natural products from marine sponges: a review (2009-2018)

Marine sponges are productive sources of bioactive secondary metabolites with over 200 new compounds isolated each year, contributing 23% of approved marine drugs so far. This review describes statistical research, structural diversity, and pharmacological activity of sponge derived new natural products from 2009 to 2018. Approximately 2762 new metabolites have been reported from 180 genera of sponges this decade, of which the main structural types are alkaloids and terpenoids, accounting for 50% of the total. More than half of new molecules showed biological activities including cytotoxic, antibacterial, antifungal, antiviral, anti-inflammatory, antioxidant, enzyme inhibition, and antimalarial activities. As summarized in this review, macrolides and peptides had higher proportions of new bioactive compounds in new compounds than other chemical classes. Every chemical class displayed cytotoxicity as the dominant activity. Alkaloids were the major contributors to antibacterial, antifungal, and antioxidant activities while steroids were primarily responsible for pest resistance activity. Alkaloids, terpenoids, and steroids displayed the most diverse biological activities. The statistic research of new compounds by published year, chemical class, sponge taxonomy, and biological activity are presented. Structural novelty and significant bioactivities of some representative compounds are highlighted. Marine sponges are rich sources of novel bioactive compounds and serve as animal hosts for microorganisms, highlighting the undisputed potential of sponges in the marine drugs research and development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00132-3.

Coculturing of Mucor plumbeus and Bacillus subtilis bacterium as an efficient fermentation strategy to enhance fungal lipid and gamma-linolenic acid (GLA) production

This study aimed to improve lipid and gamma-linolenic acid (GLA) production of an oleaginous fungus, Mucor plumbeus, through coculturing with Bacillus subtilis bacteria, optimising the environmental and nutritional culture conditions, and scaling them for batch fermentation. The maximum levels of biomass, lipid, fatty acid, and GLA in a 5 L bioreactor containing cellobiose and ammonium sulfate as the optimal carbon and nitrogen sources, respectively, achieved during the coculturing processes were 14.5 ± 0.4 g/L, 41.5 ± 1.3, 24 ± 0.8, and 20 ± 0.5%, respectively. This strategy uses cellobiose in place of glucose, decreasing production costs. The nutritional and abiotic factor results suggest that the highest production efficiency is achieved at 6.5 pH, 30 °C temperature, 10% (v/v) inoculum composition, 200 rpm agitation speed, and a 5-day incubation period. Interestingly, the GLA concentration of cocultures (20.0 ± 0.5%) was twofold higher than that of monocultures (8.27 ± 0.11%). More importantly, the GC chromatograms of cocultures indicated the presence of one additional peak corresponding to decanoic acid (5.32 ± 0.20%) that is absent in monocultures, indicating activation of silent gene clusters via cocultivation with bacteria. This study is the first to show that coculturing of Mucor plumbeus with Bacillus subtilis is a promising strategy with industrialisation potential for the production of GLA-rich microbial lipids and prospective biosynthesis of new products.

New Insights into Chemical and Biological Properties of Funicone-like Compounds

Funicone-like compounds are a homogeneous group of polyketides that, so far, have only been reported as fungal secondary metabolites. In particular, species in the genus Talaromyces seem to be the most typical producers of this group of secondary metabolites. The molecular structure of funicone, the archetype of these products, is characterized by a γ-pyrone ring linked through a ketone group to a α-resorcylic acid nucleus. This review provides an update on the current knowledge on the chemistry of funicone-like compounds, with special emphasis on their classification, occurrence, and diverse biological activities. In addition, their potential relevance as mycotoxins is discussed.

The role of bacterial signaling networks in antibiotics response and resistance regulation

Excessive use of antibiotics poses a threat to public health and the environment. In ecosystems, such as the marine environment, antibiotic contamination has led to an increase in bacterial resistance. Therefore, the study of bacterial response to antibiotics and the regulation of resistance formation have become an important research field. Traditionally, the processes related to antibiotic responses and resistance regulation have mainly included the activation of efflux pumps, mutation of antibiotic targets, production of biofilms, and production of inactivated or passivation enzymes. In recent years, studies have shown that bacterial signaling networks can affect antibiotic responses and resistance regulation. Signaling systems mostly alter resistance by regulating biofilms, efflux pumps, and mobile genetic elements. Here we provide an overview of how bacterial intraspecific and interspecific signaling networks affect the response to environmental antibiotics. In doing so, this review provides theoretical support for inhibiting bacterial antibiotic resistance and alleviating health and ecological problems caused by antibiotic contamination.

Secondary Metabolite Variation and Bioactivities of Two Marine Aspergillus Strains in Static Co-Culture Investigated by Molecular Network Analysis and Multiple Database Mining Based on LC-PDA-MS/MS

Co-culture is known as an efficient way to explore the metabolic potential of fungal strains for new antibiotics and other therapeutic agents that could counter emerging health issues. To study the effect of co-culture on the secondary metabolites and bioactivities of two marine strains, Aspergillus terreus C23-3 and Aspergillus. unguis DLEP2008001, they were co-cultured in live or inactivated forms successively or simultaneously. The mycelial morphology and high-performance thin layer chromatography (HPTLC) including bioautography of the fermentation extracts were recorded. Furthermore, the agar cup-plate method was used to compare the antimicrobial activity of the extracts. Based on the above, liquid chromatography-photodiode array-tandem mass spectrometry (LC-PDA-MS/MS) together with Global Natural Products Social molecular networking (GNPS) and multiple natural products database mining were used to further analyze their secondary metabolite variations. The comprehensive results showed the following trends: (1) The strain first inoculated will strongly inhibit the growth and metabolism of the latter inoculated one; (2) Autoclaved A. unguis exerted a strong inducing effect on later inoculated A. terreus, while the autoclaved A. terreus showed high stability of its metabolites and still potently suppressed the growth and metabolism of A. unguis; (3) When the two strains are inoculated simultaneously, they both grow and produce metabolites; however, the A. terreus seemed to be more strongly induced by live A. unguis and this inducing effect surpassed that of the autoclaved A. unguis. Under some of the conditions, the extracts showed higher antimicrobial activity than the axenic cultures. Totally, A. unguis was negative in response but potent in stimulating its rival while A. terreus had the opposite effect. Fifteen MS detectable and/or UV active peaks showed different yields in co-cultures vs. the corresponding axenic culture. GNPS analysis assisted by multiple natural products databases mining (PubChem, Dictionary of Natural Products, NPASS, etc.) gave reasonable annotations for some of these peaks, including antimicrobial compounds such as unguisin A, lovastatin, and nidulin. However, some of the peaks were correlated with antagonistic properties and remain as possible novel compounds without mass or UV matching hits from any database. It is intriguing that the two strains both synthesize chemical 'weapons' for antagonism, and that these are upregulated when needed in competitive co-culture environment. At the same time, compounds not useful in this antagonistic setting are downregulated in their expression. Some of the natural products produced during antagonism are unknown chlorinated metabolites and deserve further study for their antimicrobial properties. In summary, this study disclosed the different responses of two Aspergillus strains in co-culture, revealed their metabolic variation, and displayed new opportunities for antibiotic discovery.

A new butenolide with antifungal activity from solid co-cultivation of Irpex lacteus and Nigrospora oryzae

A new antifungal butenolide irperide (1) along with five known compounds were isolated from the co-culture of endophyte Irpex lacteus and pathogenic Nigrospora oryzae. The structure of 1, including the absolute configuration, was elucidated by analysis of NMR, HR-ESI-MS data and ECD spectra. Compounds 1, 4 and 6 exhibited significant antifungal activity against Aspergillus fumigatus, with MIC values of 1, 2 and 1 μg/mL, respectively.

Antimicrobial and Antioxidant Polyketides from a Deep-Sea-Derived Fungus Aspergillus versicolor SH0105

Fifteen polyketides, including four new compounds, isoversiol F (1), decumbenone D (2), palitantin B (7), and 1,3-di-O-methyl-norsolorinic acid (8), along with 11 known compounds (3-6 and 9-15), were isolated from the deep-sea-derived fungus Aspergillus versicolor SH0105. Their structures and absolute configurations were determined by comprehensive spectroscopic data, including 1D and 2D NMR, HRESIMS, and ECD calculations, and it is the first time to determine the absolute configuration of known decumbenone A (6). All of these compounds were evaluated for their antimicrobial activities against four human pathogenic microbes and five fouling bacterial strains. The results indicated that 3,7-dihydroxy-1,9-dimethyldibenzofuran (14) displayed obvious inhibitory activity against Staphylococcus aureus (ATCC 27154) with the MIC value of 13.7 μM. In addition, the antioxidant assays of the isolated compounds revealed that aspermutarubrol/violaceol-I (15) exhibited significant 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity with the IC50 value of 34.1 μM, and displayed strong reduction of Fe3+ with the ferric reducing antioxidant power (FRAP) value of 9.0 mM under the concentration of 3.1 μg/mL, which were more potent than ascorbic acid.