Fungi from the extremes of life: an untapped treasure for bioactive compounds

Evaluation of the Crosstalk Between the Host Mycobiome and Bacteriome in Patients with Chronic Pancreatitis

The human microbiome is a diverse consortium of microbial kingdoms that play pivotal roles in host health and diseases. We previously reported a dysbiotic bacteriome in chronic pancreatitis patients with diabetes (CPD) compared with patients with it's nondiabetic (CPND) phenotype. In this study, we extended our exploration to elucidate the intricate interactions between the mycobiome, bacteriome, and hosts' plasma metabolome with the disease phenotypes. A total of 25 participants (CPD, n = 7; CPND, n = 10; healthy control, n = 8) were recruited for the study. We observed elevated species richness in both the bacterial and fungal profiles within the CP diabetic cohort compared to the nondiabetic CP phenotype and healthy control cohorts. Notably, the CP group displayed heterogeneous fungal diversity, with only 40% of the CP nondiabetic patients and 20% of the CP diabetic patients exhibiting common core gut fungal profiles. Specific microbial taxa alterations were identified, including a reduction in Bifidobacterium adolescentis and an increase in the prevalence of Aspergillus penicilloides and Klebsiella sp. in the disease groups. In silico analysis revealed the enrichment of pathways related to lipopolysaccharide (LPS), apoptosis, and peptidase, as well as reduced counts of the genes responsible for carbohydrate metabolism in the CP groups. Additionally, distinct plasma metabolome signatures were observed, with CPD group exhibiting higher concentrations of sugars and glycerolipids, while the CPND cohort displayed elevated levels of amino acids in their blood. The fatty acid-binding protein (FABP) concentration was notably greater in the CPD group than in the HC group (4.220 vs. 1.10 ng/ml, p = 0.04). Furthermore, compared with healthy controls, disease groups exhibited fewer correlations between key fungal taxa (Aspergillus sp., Candida sp.) and bacterial taxa (Prevotella copri, Bifidobacteria sp., Rumminococcaceae). Our study unveils, for the first time, a dysbiotic mycobiome and emphasizes unique host bacterial-mycobial interactions in CP patient with diabetes, potentially influencing disease severity. These findings provide crucial insights for future mechanistic studies aiming to unravel the determinants of disease severity in this complex clinical context.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01207-8.

Aspergillus nidulans gfdB, Encoding the Hyperosmotic Stress Protein Glycerol-3-phosphate Dehydrogenase, Disrupts Osmoadaptation in Aspergillus wentii

The genome of the osmophilic Aspergillus wentii, unlike that of the osmotolerant Aspergillus nidulans, contains only the gfdA, but not the gfdB, glycerol 3-phosphate dehydrogenase gene. Here, we studied transcriptomic changes of A. nidulans (reference strain and ΔgfdB gene deletion mutant) and A. wentii (reference strain and An-gfdB expressing mutant) elicited by high osmolarity. A. nidulans showed a canonic hyperosmotic stress response characterized by the upregulation of the trehalose and glycerol metabolism genes (including gfdB), as well as the genes of the high-osmolarity glycerol (HOG) map kinase pathway. The deletion of gfdB caused only negligible alterations in the transcriptome, suggesting that the glycerol metabolism was flexible enough to compensate for the missing GfdB activity in this species. A. wentii responded differently to increased osmolarity than did A. nidulans, e.g., the bulk upregulation of the glycerol and trehalose metabolism genes, along with the HOG pathway genes, was not detected. The expression of An-gfdB in A. wentii did not abolish osmophily, but it reduced growth and caused much bigger alterations in the transcriptome than did the missing gfdB gene in A. nidulans. Flexible glycerol metabolism and hence, two differently regulated gfd genes, may be more beneficial for osmotolerant (living under changing osmolarity) than for osmophilic (living under constantly high osmolarity) species.

Fungi in Rice Field Open Irrigation System: Ecological Implications and Biosecurity

Italy is the leading producer of rice in Europe, but this crop is increasingly threatened by many factors such as pathogens' resistance, pollution and climate change. To date, few works keep in consideration the ecological role that the open irrigation system can play in the dispersion of important opportunistic species, and if it is affected by agricultural management and environmental seasonal changing. This work carried out the mycological characterization of a rice field irrigation system located in Vistarino (Pavia, Lombardy, Italy). Three main sections of an irrigation system (canal, ditch and paddy) were sampled during the summer 2018 (irrigation season of the rice crop). Water samples processing underlined how the irrigation system is rich of fungal diversity (59 species isolated). In order of abundance, the canal samples are characterized by the dominance of Aspergillus, Cladosporium, Fusarium and Trichoderma genera, while the ditch samples by Alternaria, Cladosporium, Fusarium, and Penicillium genera, and the paddy samples by Alternaria, Cladosporium, Fusarium and Trichoderma genera. Results showed that the three environments are mycologically independent of each other: fungi do not exploit the irrigation system for their dispersion in paddy. Probably fungi prefer others dispersion systems such as air dispersion. This means that an open irrigation system is not to be considered as a continue system with free circulation of fungi. Indeed, each sector of the system appears characterized by a typical funga, which undergoes variations during the sampled season due to agricultural management and environmental conditions.

The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview

Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.

The Role of Osmolytes and Membrane Lipids in the Adaptation of Acidophilic Fungi

Acidophiles maintain near-neutral intracellular pH using proton pumps. We have suggested the protective role of osmolytes and membrane lipids in the adaptation to an acidic environment. Previously we have observed, for the first time, high levels of trehalose in acidophilic basidiomycete Sistotrema brinkmannii. Here, we have studied the composition of both osmolytes and membrane lipids of two more acidophilic fungi. Trehalose and polyols were among the main osmolytes during growth under optimal conditions (pH 4.0) in basidiomycete Phlebiopsis gigantea and ascomycete Mollisia sp. Phosphatidic acids, phosphatidylethanolamines, phosphatidylcholines, and sterols, were predominant membrane lipids in both fungi. P. gigantea had a narrow optimum of growth at pH 4.0, resulting in a sharp decline of growth rate at pH 2.6 and 5.0, accompanied by a decrease in the number of osmolytes and significant changes in the composition of membrane lipids. In contrast, Mollisia sp. had a broad optimal growth range (pH 3.0-5.0), and the number of osmolytes either stayed the same (at pH 6.0) or increased (at pH 2.6), while membrane lipids composition remained unchanged. Thus, the data obtained indicate the participation of osmolytes and membrane lipids in the adaptation of acidophilic fungi.

Microbial and Plant Derived Low Risk Pesticides Having Nematocidal Activity

Microorganisms, virus, weeds, parasitic plants, insects, and nematodes are among the enemies that induce severe economic losses to agrarian production. Farmers have been forced to combat these enemies using different methods, including mechanical and agronomic strategies, since the beginning of agriculture. The development of agriculture, due to an increased request for food production, which is a consequence to the rapid and noteworthy growth of the world's population, requires the use of more efficient methods to strongly elevate the yield production. Thus, in the last five-to-six decades, a massive and extensive use of chemicals has occurred in agriculture, resulting in heavy negative consequences, such as the increase in environmental pollution and risks for human and animal health. These problems increased with the repetition of treatments, which is due to resistance that natural enemies developed against this massive use of pesticides. There are new control strategies under investigation to develop products, namely biopesticides, with high efficacy and selectivity but based on natural products which are not toxic, and which are biodegradable in a short time. This review is focused on the microbial and plant metabolites with nematocidal activity with potential applications in suitable formulations in greenhouses and fields.

Exophilone, a Tetrahydrocarbazol-1-one Analogue with Anti-Pulmonary Fibrosis Activity from the Deep-Sea Fungus Exophiala oligosperma MCCC 3A01264

A new compound, exophilone (1), together with nine known compounds (2–10), were isolated from a deep-sea-derived fungus, Exophiala oligosperma. Their chemical structures, including the absolute configuration of 1, were elucidated using nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionization mass spectroscopy (HRESIMS), and electronic circular dichroism (ECD) calculation. Compounds were preliminarily screened for their ability to inhibit collagen accumulation. Compounds 1, 4, and 7 showed weaker inhibition of TGF-β1-induced total collagen accumulation in compared with pirfenidone (73.14% inhibition rate). However, pirfenidone exhibited cytotoxicity (77.57% survival rate), while compounds 1, 4, and 7 showed low cytotoxicity against the HFL1 cell line. Particularly, exophilone (1) showed moderate collagen deposition inhibition effect (60.44% inhibition rate) and low toxicity in HFL1 cells (98.14% survival rate) at a concentration of 10 μM. A molecular docking study suggests that exophilone (1) binds to both TGF-β1 and its receptor through hydrogen bonding interactions. Thus, exophilone (1) was identified as a promising anti-pulmonary fibrosis agent. It has the potential to be developed as a drug candidate for pulmonary fibrosis.

Isolation and Characterization of a Novel Hydrophobin, Sa-HFB1, with Antifungal Activity from an Alkaliphilic Fungus, Sodiomyces alkalinus

The adaptations that alkaliphilic microorganisms have developed due to their extreme habitats promote the production of active natural compounds with the potential to control microorganisms, causing infections associated with healthcare. The primary purpose of this study was to isolate and identify a hydrophobin, Sa-HFB1, from an alkaliphilic fungus, Sodiomyces alkalinus. A potential antifungal effect against pathogenic and opportunistic fungi strains was determined. The MICs of Sa-HFB1 against opportunistic and clinical fungi ranged from 1 to 8 µg/mL and confirmed its higher activity against both non- and clinical isolates. The highest level of antifungal activity (MIC 1 µg/mL) was demonstrated for the clinical isolate Cryptococcus neoformans 297 m. The hydrophobin Sa-HFB1 may be partly responsible for the reported antifungal activity of S. alkalinus, and may serve as a potential source of lead compounds, meaning that it can be developed as an antifungal drug candidate.

Antimicrobial Properties and the Effect of Temperature on the Formation of Secondary Metabolites in Psychrophilic Micromycetes

Abstract

The ability of representatives of psychrotolerant micromycetes to produce antimicrobial compounds was studied. A promising producer of antibiotics, Penicillium vulpinum KPB F-290, was selected (from 98 cultures) as a result of the screening. The producer was active against opportunistic fungi and bacteria. The isolated active fractions can be attributed to the group of antimicrobial compounds, including ß-lactam antibiotics and peptides.

Stress Dependent Biofilm Formation and Bioactive Melanin Pigment Production by a Thermophilic Bacillus Species from Chilean Hot Spring

Thermophilic bacteria able to survive extreme temperature stress are of great biotechnological interest due to their extracellular production of bioactive molecules as a part of a survival strategy, or by intracellular modifications. In the present study, thermophilic Bacillus haynesii CamB6, isolated from a Chilean hot spring, was studied for the formation of different stress response molecules. The polymeric pigment produced by the bacterial strain was characterized by different physicochemical techniques. On exposure to ranges of temperature (50–60 °C), pH (5.0–7.0), and sources of nitrogen and carbon (1–5 g·L⁻¹), the bacteria responded with a biofilm network formation in a hydrophobic polystyrene surface. Biofilm formation under fed-batch conditions was also statistically validated. The bacteria showed a planktonic pellicle network formation in the presence of induced hypoxia and salinity stress (19.45 g·L⁻¹) under static conditions. Salinity stress also resulted in the intracellular response of brown pigment production. The pigment was structurally and functionally characterized by UV-Vis absorbance and the presence of different characteristic peaks via FTIR analysis (bacterial pyomelanin fingerprints) were assessed. A high thermal stability and TGA profile indicated the brown pigment was a probable pyomelanin candidate. Micropyrolysis (Py-GC/MS) showed that isoprene, pyrrole, benzene, pyridine, and their derivatives were the major components detected. In addition, acetic acid, indole, phenol, and its derivatives were observed. The absence of sulfocompounds in the pyrolyzed products agreed with those reported in the literature for pyomelanin. The pigment surface morphology was analyzed via SEM, and the elemental composition via EDS also demonstrated the similarity of the brown pigment to that of the melanin family. The pyomelanin pigment was observed to be bioactive with promising antioxidant capacity (H₂O₂, Fe²⁺) compared to the standard antioxidant molecules. In conclusion, B. haynesii CamB6 demonstrated the formation of several biomolecules as a stress response mechanism that is bioactive, showing its probable biotechnological applications in future.

Potentials of Endophytic Fungi in the Biosynthesis of Versatile Secondary Metabolites and Enzymes

World population growth and modernization have engendered multiple environmental problems: the propagation of humans and crop diseases and the development of multi-drug-resistant fungi, bacteria and viruses. Thus, a considerable shift towards eco-friendly products has been seen in medicine, pharmacy, agriculture and several other vital sectors. Nowadays, studies on endophytic fungi and their biotechnological potentials are in high demand due to their substantial, cost-effective and eco-friendly contributions in the discovery of an array of secondary metabolites. For this review, we provide a brief overview of plant–endophytic fungi interactions and we also state the history of the discovery of the untapped potentialities of fungal secondary metabolites. Then, we highlight the huge importance of the discovered metabolites and their versatile applications in several vital fields including medicine, pharmacy, agriculture, industry and bioremediation. We then focus on the challenges and on the possible methods and techniques that can be used to help in the discovery of novel secondary metabolites. The latter range from endophytic selection and culture media optimization to more in-depth strategies such as omics, ribosome engineering and epigenetic remodeling.

Isolation of Taxol and Flavin-like fluorochrome from Endophytic Fungi of Mangifera indica

Scouting for novel and plant-derived biomolecules from endophytic microbial sources draws greater focus on the discovery of novel bioactive metabolites. With this rationale, we scouted the endophytic fungi for taxol, an anticancer diterpenoid and fluorescent biomolecules. In the present study, about 31 endophytic fungal isolates recovered from the Mangifera indica leaves were screened for taxol production in M1D medium. About five isolates were shortlisted based on the thin layer chromatographic analysis of the fungal extracts. Among them Colletotrichum sp. MIP-5 has been identified as a producer of fungal taxol based on UV, FTIR, TLC and HPLC analysis. The partially purified fungal taxol showed similar spectral and chromatographic features of commercially available paclitaxel. In addition to this, we also report the production of a fluorescent compound by Penicillium sp. MIP-3. The Flavin-like compound exhibited a bright greenish-yellow fluorescence with an emission maximum in the range of 505 – 545nm. GC-MS analysis showed the occurrence of Latia luciferin, primarily associated with the bioluminescence of freshwater limpet Latia neritoides. This is the first report of this compound from Penicillium sp. In addition, therapeutically active steroid (β-Sitosterol, Stigmasterol, Campesterol), quinones (Benzo[h]quinoline, 2,4-dimethyl-) and phloroglucinol (Aspidinol) derivatives were also identified from Penicillium sp. MIP-3 based on GC-MS analysis. These molecules could potentially be used in biological and pharmaceutical applications in future.

Research Progress in Anti-Inflammatory Bioactive Substances Derived from Marine Microorganisms, Sponges, Algae, and Corals

Inflammation is the body’s defense reaction in response to stimulations and is the basis of various physiological and pathological processes. However, chronic inflammation is undesirable and closely related to the occurrence and development of diseases. The ocean gives birth to unique and diverse bioactive substances, which have gained special attention and been a focus for anti-inflammatory drug development. So far, numerous promising bioactive substances have been obtained from various marine organisms such as marine bacteria and fungi, sponges, algae, and coral. This review covers 71 bioactive substances described during 2015–2020, including the structures (65 of which), species sources, evaluation models and anti-inflammatory activities of these substances. This review aims to provide some reference for the research progress of marine-organism-derived anti-inflammatory metabolites and give more research impetus for their conversion to novel anti-inflammatory drugs.

Screening and isolation of microbes from a Mud Community of Ischia Island Thermal Springs: preliminary analysis of a bioactive compound

Introduction

Balneotherapy centers of Ischia island (Italy) offer treatments for different dermatological diseases (psoriasis, acne, atopic dermatitis) and upper respiratory tract infections. In this study, we integrated morphological and molecular approaches to give a focus on isolation and screening of extremophile bacteria from Ischia thermal mud for potential antimicrobial applications.

Methods

Samples were collected during 2019 at four sites. Some bacterial strains ATCC for antibacterial and antibiofilm activity were tested. After morphological characterization, screening for antagonistic isolates was made. The colonies isolated from thermal mud samples were submitted to molecular characterization. Susceptibility testing by dilution spotting was carried out and antibacterial efficacies of most active isolate were evaluated with a Minimal inhibition concentration assay. Biofilm formation, inhibition, eradication were examined. Statistical analyses were carried out utilizing Microsoft^® Excel 2016/XLSTAT^©-Pro.

Results

We isolated a natural compound with antimicrobial and antibiofilm activities.

Conclusions

The results obtained in this study are discussed in the context of how hydrothermal systems are important environmental source of uncharted antimicrobial and antibiofilm compounds. In conclusion, to the most effective of our knowledge, this work presents the primary report on the preliminary investigation of thermophile microbial diversity and their antimicrobial and antibiofilm activities for future biotechnological interest.

Rare Chromone Derivatives from the Marine-Derived Penicillium citrinum with Anti-Cancer and Anti-Inflammatory Activities

Three new and rare chromone derivatives, epiremisporine C (1), epiremisporine D (2), and epiremisporine E (3), were isolated from marine-derived Penicillium citrinum, together with four known compounds, epiremisporine B (4), penicitrinone A (5), 8-hydroxy-1-methoxycarbonyl-6-methylxanthone (6), and isoconiochaetone C (7). Among the isolated compounds, compounds 2–5 significantly decreased fMLP-induced superoxide anion generation by human neutrophils, with IC₅₀ values of 6.39 ± 0.40, 8.28 ± 0.29, 3.62 ± 0.61, and 2.67 ± 0.10 μM, respectively. Compounds 3 and 4 exhibited cytotoxic activities with IC₅₀ values of 43.82 ± 6.33 and 32.29 ± 4.83 μM, respectively, against non-small lung cancer cell (A549), and Western blot assay confirmed that compounds 3 and 4 markedly induced apoptosis of A549 cells, through Bcl-2, Bax, and caspase 3 signaling cascades.

Antimicrobial Potential of the Alkalophilic Fungus Sodiomyces alkalinus and Selection of Strains–Producers of New Antimicotic Compound

Abstract

The ability of alkalophilic micromycetes of the species Sodiomyces alkalinus to produce antimicrobial compounds was studied. As a result of the determination of the spectrum and yield of antibiotic compounds, a promising producer of the antimycotics Sodiomyces alkalinus was selected from the most active strains 8KS17-10. The producer exhibited antifungal activity against opportunistic fungi, as well as pathogenic clinical isolates of molds and yeasts—pathogens of systemic mycoses. The isolated active compound can be attributed to the group of antimicrobial glycopeptides based on the totality of the identified structural features (molecular weight, absorption ratio at certain wavelengths).

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Progress in Research on Bioactive Secondary Metabolites from Deep-Sea Derived Microorganisms

Deep sea has an extreme environment which leads to biodiversity of microorganisms and their unique physical and biochemical mechanisms. Deep-sea derived microorganisms are more likely to produce novel bioactive substances with special mechanism of action for drug discovery. This article reviews secondary metabolites with biological activities such as anti-tumor, anti-bacterial, anti-viral, and anti-inflammatory isolated from deep-sea fungi and bacteria during 2018-2020. Effective methods for screening and obtaining natural active compounds from deep-sea microorganisms are also summarized, including optimizing the culture conditions, using genome mining technology, biosynthesis and so on. The comprehensive application of these methods makes broader prospects for the development and application of deep sea microbial bioactive substances.

Fungal benzene carbaldehydes: occurrence, structural diversity, activities and biosynthesis

Covering: up to April 2020Fungal benzene carbaldehydes with salicylaldehydes as predominant representatives carry usually hydroxyl groups, prenyl moieties and alkyl side chains. They are found in both basidiomycetes and ascomycetes as key intermediates or end products of various biosynthetic pathways and exhibit diverse biological and pharmacological activities. The skeletons of the benzene carbaldehydes are usually derived from polyketide pathways catalysed by iterative fungal polyketide synthases. The aldehyde groups are formed by direct PKS releasing, reduction of benzoic acids or oxidation of benzyl alcohols.