Relation of Pythium oligandrum Drechsler to bacteria, Actinomyces, and several fungi inhabiting the rhizosphere of the emerging sugar-beet.
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Antibiosis↗
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Results for “emerging fungi”
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First draft genome sequence of the emerging sexually transmitted dermatophyte Trichophyton mentagrophytes genotype VII.
Trichophyton mentagrophytes ITS-genotype VII (TMVII) is a globally emerging sexually transmitted dermatophyte causing severe skin infections characterised by painful, pustular lesions on the face, public area, genitalia, and trunk. To inform the prevention efforts, we present the first draft genomes of four TMVII isolates obtained from patients in the United Kingdom diagnosed between 2021 and 2025. We performed whole-genome sequencing and phylogenetic analysis based on single-nucleotide polymorphisms. We analysed the genetic relatedness of four TMVII isolates collected from UK patients, two had travel links to Spain and the Middle East. Two further isolates, including T. mentagrophytes ITS-genotype I/II obtained from a canine infection in the United Kingdom in 2025 and Trichophyton indotineae were sequenced for contextual analysis. We confirm that the TMVII strains studied here represent a highly clonal population, distinct from both zoophilic T. mentagrophytes genotype I/II and anthropophilic T. indotineae.
Humans↗
Activation of secondary metabolism in Aspergillus and related filamentous fungi through regulatory engineering.
Filamentous fungi are major contributors to diverse secondary metabolites with broad applications to medicine, agriculture, and biotechnology. Advances in genome sequencing and bioinformatic tools have revealed that fungal genomes encode far more biosynthetic gene clusters (BGCs) than are expressed under normal laboratory conditions, leaving much biosynthetic potential transcriptionally silent. Overcoming this gap between predicted and observed secondary metabolism has become a major challenge in fungal natural product discovery. In this review, we summarize current strategies for activating silent or weakly expressed fungal BGCs through regulatory engineering, with an emphasis on approaches validated in Aspergillus, Penicillium, Monascus, and related filamentous fungi. We focus on genetic and chemical manipulations that enable coordinated activation of multiple biosynthetic pathways through chromatin-level modifiers, global transcriptional regulators, and developmental regulators. By framing these regulators as practical tools rather than solely biological components, we demonstrate their strengths, limitations, and applications in Aspergillus and related filamentous fungi. We further discuss emerging combinatorial and integrative approaches that use regulatory engineering alongside omics technologies and predictive tools, outlining alternatives and future directions for improving the interpretability of silent pathway activation.
Journal Article↗
Development of amphotericin B-resistant Candida tropicalis in a patient with defective leukocyte function.
Emergence, during therapy, of fungi resistant to amphotericin B is purportedly rare, as fungi with altered cell membrane ergosterol content are considered too fragile to survive normal host defenses. Progressive amphotericin B resistance arose in a strain of Candida tropicalis isolated repeatedly from the urine of a patient with pyelonephritis. The most resistant isolate (R-2) lacked cell membrane ergosterol, the usual attachment site for amphotericin B, and was not inhibited by greater than 500 micrograms/ml of the drug. R-2 infected and killed embryonated eggs, but was unable to produce progressive renal infection in steroid-treated mice because of a reduced capacity to produce pseudomycelia. Persistent infection of the patient by this altered fungus was attributed to defective leukocyte candidacidal activity, especially marked in autologous serum, and to defective Candida-related cell-mediated immunity. A literature review suggests that amphotericin B resistance may not be as rare as many authorities have indicated. It is apparent that few laboratories routinely monitor fungi for amphotericin B susceptibility. In patients with defective antimicrobial defenses, amphotericin B-resistant fungi may survive, produce progressive infection, and require alternative chemotherapy for eradication.
Amphotericin B↗
The deoxyribonucleic acid polymerases of non-vertebrate eukaryotes.
DNA-dependent DNA polymerases have now been purified from a number of invertebrate animals, protists, higher plants and fungi. In this article we review the properties of these enzymes and compare them with the better-known enzymes of vertebrate animals and prokaryotes. Three facts emerge. Firstly, plants, protists and fungi contain high-molecular-weight DNA polymerases which may be capable of categorization into two groups on the basis of their properties in vitro. Secondly, no enzyme analogous to the vertebrate polymerase-beta has yet been found in such organisms, and thirdly, many of these enzymes possess associated exonuclease activities like those of the bacterial DNA polymerases. On the basis of these findings, some tentative proposals are made about the evolution of DNA polymerases.
Animals↗
Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans.
Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system in Cryptococcus neoformans that enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify the C. neoformans genome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studied RIM101 pathway in fluconazole susceptibility. We also show that insertions of transposons into the 5' upstream region can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5' insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies of C. neoformans, particularly in examining the consequences of genotypic diversity.
Cryptococcus neoformans↗
Mycodnaviridae is a clade of giant viruses that persistently infect zoosporic fungi.
Giant viruses of the phylum Nucleocytoviricota have emerged as particularly notable due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes, and they have been detected in hosts that span the eukaryotic tree of life. But surprisingly, such viruses have not been definitively found in Kingdom Fungi, though earlier genomic and metagenomic work suggests putative associations. Here we report both "viral fossils" and active infection by giant viruses in fungi, particularly in the zoosporic phyla Blastocladiomycota and Chytridiomycota. The recovered viral assemblies span up to 350 kb, encode over 300 genes, and form a monophyletic family-level clade within the Nucleocytoviricota related to orders Imitervirales and Algavirales, which we name Mycodnaviridae. We observed variation in infection status among the isolates including apparent active infection and transcriptionally suppressed states, suggesting that viral activation may be constrained to certain life stages of the host. Our experimental findings add to the limited natural virus-host systems available in culture for the study of giant viruses and expand the known host range of Nucleocytoviricota into a new kingdom that contains many model species. Mycodnaviridae have a global distribution, which invites inquiry into the implications of these infections for host traits, host genome evolution, and the metabolic impacts on ecosystems.
Giant Viruses↗
Parasitic relationships between Pythium oligandrum Drechsler and some other species of the Oomycetes class.
Parasitic relationships between Pythium oligandrum Drechsler and some phytopathogenic species of the Oomycetes class were investigated on agar plates. A high parasitic ability of Pythium oligandrum on Pythium ultimum Trow, P. debaryanum Hesse, and Aphanomyces laevis De By species was proved in this study of relationships among these fungi, commonly populating the rhizosphere of emerging sugar beet. P. oligandrum produces numerous thin haustorial threads, searching the hyphae of host species and enwrapping them during the parasitation. In a later parasitation stage the host organs were enwrapped by thicker hyphae of P. oligandrum as well. P. oligandrum grew through the colony of parasitized species mostly within 24 hours after inoculation and was able to destroy it entirely within 5--6 days. P. oligandrum produced numerous fructification organs in contradistinction to parasitized species. P. oligandrum oospores germinated abundantly when host species were present. Hyperparasitism of P. oligandrum was found both in cultivation with a single host and in common cultivation with all three host species simultaneously.
Agar↗
Fungi to the rescue: recent advances, mechanistic insights and omics-based perspectives in heavy metal mycoremediation.
Heavy metal (HM) contamination arising from rapid industrialization poses critical threats to global ecosystem integrity and public health. Conventional physicochemical approaches are limited by high costs, incomplete removal, and toxic waste generation, necessitating sustainable alternatives. Mycoremediation, which harnesses the remarkable, diverse capacities of fungi to tolerate and mitigate HM stress through sophisticated biological mechanisms, has emerged as a promising and sustainable approach to address HM pollution. This review examines the sources and ecotoxicological impacts of HM pollution, alongside the intracellular and extracellular mechanisms underlying fungal tolerance and removal, including biosorption, precipitation, membrane transport, antioxidant defense, chelation, bioaccumulation, and biotransformation. It further synthesizes fungal-based bioremediation strategies, while examining how metagenomic, metatranscriptomic, transcriptomic, proteomic, and metabolomic approaches are advancing understanding of fungal community structure and active detoxification pathways. This work uniquely integrates community- and isolate-level multi-omics data, explicitly bridges mechanistic understanding with omics-driven insights, and extends this into translational roadmap for applied bioremediation.
Biodegradation, Environmental↗
Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.
Microbial symbiosis underpins host adaptation, yet mechanisms of metabolic integration in holobionts remain unclear. Using metatranscriptomics, genomics, and metabolic assays, we investigated gut microbiome interactions in the European spruce bark beetle (Ips typographus). We observed metabolic complementarity among symbionts and host, forming cross-domain networks that support nutrient acquisition. Nitrogen recycling revealed strong interdependence: no single partner possessed a complete uric acid degradation pathway, but combined evidence supports a distributed pathway spanning beetle, Bacteria, and fungi. Additionally, bacterial nitrate reduction to ammonia indicates a potential nitrogen influx, making otherwise inaccessible inorganic nitrogen available to the host. Shaped by microbial interactions, symbionts also likely supply specific amino acids, while vitamin metabolism showed cross-domain co-metabolism, with Bacteria as main producers of B vitamins, while host and fungi modulated interconversion. Carbohydrate degradation was highly partitioned; bacteria target xylan and pectin, while fungi contribute to glucan breakdown. Crucially, our data provide indirect evidence that the beetle may contribute to complete cellulose degradation, highlighting an underappreciated host role in lignocellulose processing. In terms of enzymatic functional diversity, the bacteriome emerged as the most important microbiome component-an observation that contrasts with the traditional focus on fungi and underscores the need to consider bacterial contributions in insect symbioses. Despite life-stage variation, core metabolic functions remained stable. Overall, metabolic interdependence, rather than microbial composition alone, structures holobiont function. These results highlight functional redundancy and ecological resilience, emphasizing the importance of microbial cooperation and host-microbe metabolic evolution.
Bark beetle↗
An overview of the use of proteomics and peptidomics to characterize alternative protein foods.
The global protein transition is accelerating the development of alternative protein foods, mainly derived from plants, insects, algae, fungi, and cellular agriculture. Ensuring the authenticity, safety, and nutritional adequacy of these emerging protein matrices requires molecular-level characterization beyond traditional compositional analyses. Proteomics and peptidomics have emerged as transformative analytical platforms capable of decoding the molecular signatures that define protein origin, structural integrity, digestibility, functionality, and health potential. The review comprehensively examines the application of proteomics, and peptidomics for profiling alternative protein foods. Further, the source authentication strategies based on species-specific protein and peptide biomarkers, detection of adulteration in complex matrices, and allergenicity assessment is discussed. Special attention is also given to nutritional proteomics with protein digestibility, gastrointestinal peptide release, and identification of bioactive sequences. SIGNIFICANCE: The importance of this review is that proteomics and peptidomics are becoming central in the management of the fast-growing environment of alternative protein foods, such as plant-based, insect, algal, fungal, and cultured meat products. It provides an explanation of the application of mass spectrometry-based processes to decode molecular signatures defining the origin of proteins, their structural integrity, digestibility, allergenicity, and bioactive properties, and thus directly contribute to safety, nutritional analysis, and authenticity of the product. Presentation of the article includes the integration of the knowledge of traditional muscle foods with alternative systems of proteins, where validated protein and peptide biomarkers are used in authentication, fraud detection, and allergy risk assessment in a wide variety of matrices. It also indicates the role of nutritional proteomics and peptidomics in informing the formulation strategy to promote digestibility and release of health-promoting peptides. In general, this review will guide scientists, the food industry, and regulatory bodies to use modern proteomic technologies in quality assurance, and decision-making, for the advancementof sustainable protein-based foods.
Proteomics↗
Microbial diversity: the essential foundation for life on our planet.
The biological basis of life on Earth is microbial diversity that ensures human health, agricultural productivity, ecological balance, and ecosystem functioning. Microorganisms enable ecosystem restoration through bioremediation, maintain soil fertility, support plant growth, manage vital biogeochemical cycles, and contribute to climate resilience. Precision probiotics, postbiotics, faecal microbiota transplantation, and personalized microbiome medicine are the examples of emerging microbiome-based therapies that offer promising therapeutic opportunities. In humans, the gut microbial community is essential for immune regulation, metabolism, and disease prevention. In terrestrial ecological systems, interactions between plants, fungi, bacteria, and other soil microorganisms improve carbon sequestration, nutrient cycling, stress resilience, and sustainable agricultural productivity in the given effects of climate change. Emerging uses in agriculture, environmental restoration, and medicine are made possible by advancements in multi-omic techniques, synthetic microbial genomes, microbiome engineering, and artificial intelligence. Considering these developments, issues with ecological complexity, long-term validation, standardization, and field scale application still exist. Therefore, preserving microbial diversity is important for conserving ecological resilience and strengthening the One Health framework, which highlights the mutual dependance of health of animal, human, plant, and environment. This review summarizes what has been discovered about ecological and biomedical relevance of microbiome, identifies important research gaps, highlighting emerging technologies, and evaluates potential future directions for using microbiome to support planetary sustainability.
Bioremediation↗
Reframing the asthma microbiome: Multikingdom, multisite, and multiomic perspectives.
The field of asthma microbiome research has shifted rapidly in recent years. Advances in sequencing technology have led to an increased ability to characterize multikingdom microbial species and integration with host -omics profiling to enhance future translational applications. Traditional bacteria-centric, cross-sectional studies are giving way to mechanistic frameworks that incorporate fungi, viruses, and host-immune interactions. In this state-of-the-art review of emerging concepts in microbiome asthma research, we first propose a structured framework to consider microbiome studies across 5 major domains-microbial kingdom, site of sampling, integration with host -omics, clinical outcome domain, and translational relevance-in order to synthesize recent high-impact human microbiome studies in asthma. We highlight emerging evidence that fungal and viral communities contribute independently to asthma risk and that human microbial communities are linked to distinct inflammatory and immune pathways shaped by host genetic susceptibility.
Asthma↗
A new diagnostic unit for corneal ulcers.
A self-contained microbiologic unit has been presented as an expedient to facilitate the diagnosis of corneal ulcers in an office or emergency room. In addition, rationale for its contents are indicated. Although the commonly isolated bacteria and fungi, as well as many of the rare forms, can be cultured on the intact media included in this unit, growth of strict anaerobes may not be supported without additional processing of the media.
Bacteriological Techniques↗
The black aspergilli (Aspergillus niger complex) and their role in human, animal, and plant diseases.
SUMMARYThe Aspergillus niger complex, also known as the black aspergilli or section Nigri, comprises a diverse group of filamentous fungi with wide-ranging ecological, industrial, and pathogenic significance. While traditionally associated with food spoilage and industrial fermentation, black aspergilli have emerged as opportunistic pathogens affecting humans, animals, and plants. This review provides a comprehensive synthesis of the taxonomy, ecology, pathogenicity, and antifungal resistance of the A. niger complex. Advances in phylogenetics and whole-genome sequencing have clarified the taxonomy of section Nigri, now comprising six core species in series Nigri. Clinically, A. niger complex is implicated in various conditions, including otomycosis, keratitis, cutaneous infections, onychomycosis, chronic pulmonary aspergillosis, and, less commonly, invasive aspergillosis. In animals, black aspergilli have been isolated from respiratory, cutaneous, and systemic infections, particularly in immunocompromised or stressed hosts. Plant pathogenicity is significant, with A. niger complex contributing to pre- and post-harvest spoilage and producing mycotoxins such as ochratoxin A and oxalic acid. The common finding of elevated minimum inhibitory concentrations (MICs) to triazoles, particularly in both environmental and clinical isolates, raises concern, with underlying mechanisms differing from those characterized in A. fumigatus. Reduced susceptibility is potentially driven by efflux pumps and environmental exposure to azole fungicides. Due to commonly higher MICs, antifungal therapy with itraconazole and isavuconazole may have reduced efficacy, and alternatives such as voriconazole or posaconazole should be considered, guided by susceptibility testing where available. This review emphasizes the need for a One Health approach to managing black aspergilli, integrating surveillance, diagnostics, and targeted interventions across human, veterinary, and agricultural sectors.
Humans↗
Biological protection of emerging sugar-beet against damping-off established by mycoparasitism in non-sterilized soil.
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Antibiosis↗
Lung complications during immunosuppressive treatment in renal transplant recipients.
Pulmonary complications among 77 renal transplant recipients have been analysed. In the immediate postoperative period complications occurred with the same frequency as after other operations. Later on, usually within 6 months, pneumonia caused by bacteria, Pneumocystis carinii, cytomegalovirus and fungi occurred. The lung changes may indicate the underlying infecting organisms. Mortality from pneumonia was 14% (11/77) including two patients with lung aspiration following emergency surgery. Pulmonary complications were significantly higher in men.
Adolescent↗
Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
Genome, Fungal↗