The presence of a significant endophytic fungus in mycobiome of rice seed compartments.

Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed's compartment, indicating that the compartment can affect the distribution of the seed microbial community.

The temporal dynamics of the gut mycobiome and its association with cardiometabolic health in a nationwide cohort of 12,641 Chinese adults.

The dynamics of the gut mycobiome and its association with cardiometabolic health remain largely unexplored. Here, we employ internal transcribed spacer (ITS) sequencing to capture the gut mycobiome composition and dynamics within a nationwide human cohort of 12,641 Chinese participants, including 1,946 participants with repeated measurements across three years. We find that the gut mycobiome is associated with cardiometabolic diseases and related biomarkers in both cross-sectional and dynamic analyses. Fungal alpha diversity indices and 19 mycobiome genera are the major contributors to the mycobiome-cardiometabolic disease link. Particularly, Saccharomyces emerges as an effect modifier of traditional risk factors in promoting type 2 diabetes risk. Further integration of multi-omics data reveals key metabolites such as γ-linolenic acid and L-valine linking the gut mycobiome to type 2 diabetes. This study advances our understanding of the potential roles of the gut mycobiome in cardiometabolic health.

Metagenomic symphony of the intestinal ecosystem: How the composition affects the mind.

Mental health disorders and neurodegenerative diseases place a heavy burden on patients and societies, and, although great strides have been made to understand the pathophysiology of these conditions, advancement in drug development is lagging. The importance of gastrointestinal health in maintaining overall health and preventing disease is not a new concept. Hundreds of years ago, healers from various cultures and civilizations recognized the crucial role of the gut in sustaining health. More than a century ago, scientists began exploring the restorative effects of probiotics, marking the early recognition of the importance of gut microbes. The omics era brought more enlightenment and enabled researchers to identify the complexity of the microbial ecosystems we harbour, encompassing bacteria, eukaryotes (including fungi), archaea, viruses, and other microorganisms. The extensive genetic capacity of the microbiota is dynamic and influenced by the environment. The microbiota therefore serves as a significant entity within us, with evolutionarily preserved functions in host metabolism, immunity, development, and behavior. The significant role of the bacterial gut microbiome in mental health and neurodegenerative disorders has been realized and described within the framework of the microbiota-gut-brain axis. However, the bacterial members do not function unaccompanied, but rather in concert, and there is a substantial knowledge gap regarding the involvement of non-bacterial microbiome members in these disorders. In this review, we will explore the current literature that implicates a role for the entire metagenomic ensemble, and how their complex interkingdom relationships could influence CNS functioning in mental health disorders and neurodegenerative diseases.

Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.

Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.

Effect of diet on the gut mycobiome and potential implications in inflammatory bowel disease.

The gut microbiome is a complex, unique entity implicated in the prevention, pathogenesis, and progression of common gastrointestinal diseases. While largely dominated by bacterial populations, advanced sequencing techniques have identified co-inhabiting fungal communities, collectively referred to as the mycobiome. Early studies identified that gut inflammation is associated with altered microbial composition, known as gut dysbiosis. Altered microbial profiles are implicated in various pathological diseases, such as inflammatory bowel disease (IBD), though their role as a cause or consequence of systemic inflammation remains the subject of ongoing research. Diet plays a crucial role in the prevention and management of various diseases and is considered to be an essential regulator of systemic inflammation. This review compiles current literature on the impact of dietary modulation on the mycobiome, showing that dietary changes can alter the fungal architecture of the gut. Further research is required to understand the impact of diet on gut fungi, including the metabolic pathways and enzymes involved in fungal fermentation. Additionally, investigating whether dietary modulation of the gut mycobiome could be utilized as a therapy in IBD is essential.

The bacterial and yeast microbiota in livestock forages in Hungary.

BACKGROUND: Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe. RESULTS: We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity. CONCLUSION: Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive.

Dysbiosis of the human skin mycobiome in patients receiving systemic IL-23 inhibitors.

BACKGROUND: Systemic inhibition of pro-inflammatory cytokines affects the skin microbiome; however, the impact of systemic anti-inflammatory therapy on the skin fungal microbiome is poorly understood. To examine the effects of cytokine inhibition on the fungal community on human skin and oral mucosa, we analyzed the composition of the skin mycobiome before and after IL-23 inhibition. METHODS: The study enrolled 15 psoriasis patients. Swab samples were collected from the psoriasis-free skin of antecubital fossa, post-auricular, and the tongue surface before and after 16 weeks of treatment with anti-IL-23 antibodies. Fungal DNA was sequenced by ITS1 metagenomic analysis, and taxonomic classification was performed. RESULTS: Data from samples collected from the antecubital fossa revealed that the α diversity of the skin mycobiome decreased significantly after treatment with anti-IL-23 antibodies (p = 0.0120). Fungal DNAs were not amplified in 6/15 swab samples after 16 weeks of IL-23 inhibition; by contrast, sufficiently detected in all 15 samples before treatment (p = 0.0554). A comparison of 9/15 paired samples containing well-detected reads revealed that the percentage of genus Malassezia in the mycobiome fell significantly after treatment with IL-23 inhibitors (before, 29.3% ± 9.9%; after; 8.5% ± 3.4%, p = 0.0137). The mycobiome on post-auricular skin and on the tongue surface showed no marked changes after IL-23 inhibition. CONCLUSIONS: Taken together, the data suggest that inhibition of systemic IL-23 provokes dysbiosis of the mycobiome at the antecubital fossa skin, a finding characterized by reduced fungal diversity and a reduction in the percentage of the genus Malassezia.

Metabolome and Mycobiome of Aegilops tauschii Subspecies Differing in Susceptibility to Brown Rust and Powdery Mildew Are Diverse.

The present study demonstrated the differences in the seed metabolome and mycobiome of two Aegilops tauschii Coss accessions with different resistance to brown rust and powdery mildew. We hypothesized that the seeds of resistant accession k-1958 Ae. tauschii ssp. strangulata can contain a larger number of metabolites with antifungal activity compared with the seeds of susceptible Ae. tauschii ssp meyeri k-340, which will determine differences in the seed fungal community. Our study emphasizes the differences in the seed metabolome of the studied Ae. tauschii accessions. The resistant accession k-1958 had a higher content of glucose and organic acids, including pyruvic, salicylic and azelaic acid, as well as pipecolic acids, galactinol, glycerol and sitosterol. The seeds of Ae. tauschii-resistant accession k-1958 were found to contain more active substances with antifungal activity. The genera Cladosporium and Alternaria were dominant in the seed mycobiome of the resistant accession. The genera Alternaria, Blumeria and Cladosporium dominated in seed mycobiome of susceptible accession k-340. In the seed mycobiome of the resistant k-1958, a higher occurrence of saprotrophic micromycetes was found, and many of the micromycetes were biocontrol agents. It was concluded that differences in the seed metabolome of Ae. tauschii contributed to the determination of the differences in mycobiomes.

The role of dysbiotic gut mycobiota in modulating risk for abdominal aortic aneurysm.

Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like Candida species and a decrease in beneficial yeasts such as Saccharomyces cerevisiae. The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that Saccharomyces cerevisiae significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine. IMPORTANCE: Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful Candida species and a decrease in beneficial yeasts like Saccharomyces cerevisiae. This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with Saccharomyces cerevisiae significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures.

The airway mycobiome and interactions with immunity in health and chronic lung disease.

The existence of commensal fungi that reside within the respiratory tract, termed the airway mycobiome, has only recently been discovered. Studies are beginning to characterize the spectrum of fungi that inhabit the human upper and lower respiratory tract but heterogeneous sampling and analysis techniques have limited the generalizability of findings to date. In this review, we discuss existing studies that have examined the respiratory mycobiota in healthy individuals and in those with inflammatory lung conditions such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. Associations between specific fungi and features of disease pathogenesis are emerging but the precise functional consequences imparted by mycobiota upon the immune system remain poorly understood. It is imperative that further research is conducted in this important area as a more detailed understanding could facilitate the development of novel approaches to manipulating the mycobiome for therapeutic benefit.

Bacteria, Fungi, and Scalp Psoriasis: Understanding the Role of the Microbiome in Disease Severity.

Background: Psoriasis is a chronic skin condition affected by genetic and environmental factors. Changes in the skin microbiome may affect the immune system and skin barrier functions, thereby contributing to the development and progression of psoriasis. The scalp, which is a common site for psoriasis, is often resistant to therapy. Although several studies have investigated the scalp microbiome, analyses focusing on both bacteria and fungi remain scarce. Methods: We examined the scalp microbiomes of 11 patients with psoriasis complicated with scalp lesions and categorized them according to their Psoriasis Area Severity Index (PASI) scores. The bacterial and fungal data were analyzed using QIIME2 pipeline version 2021.04 and the UNITE database version 8.3, respectively. Results: The Shannon indices for mild (2 patients), moderate (4 patients), and severe (5 patients) groups were 0.97, 1.38, and 1.88, respectively. A significant correlation was observed between increased mycobiome diversity and disease severity (p = 4.07 × 10-5, Spearman's correlation: 0.9269). Compared with the mild and moderate groups, the severe group exhibited a higher abundance of Malassezia globosa. Pseudomonas and Staphylococcus were, respectively, more prevalent in the moderate and severe groups than in the mild group. Conclusions: This study highlights the potential role of increased fungal diversity and specific microbial compositions in the severity of scalp psoriasis, suggesting a possible avenue for targeted therapeutic interventions.

The gut-lung axis: the impact of the gut mycobiome on pulmonary diseases and infections.

The gastrointestinal tract contains a diverse microbiome consisting of bacteria, fungi, viruses and archaea. Although these microbes usually reside as commensal organisms, it is now well established that higher abundance of specific bacterial or fungal species, or loss of diversity in the microbiome can significantly affect development, progression and outcomes in disease. Studies have mainly focused on the effects of bacteria, however, the impact of other microbes, such as fungi, has received increased attention in the last few years. Fungi only represent around 0.1% of the total gut microbial population. However, key fungal taxa such as Candida, Aspergillus and Wallemia have been shown to significantly impact health and disease. The composition of the gut mycobiome has been shown to affect immunity at distal sites, such as the heart, lung, brain, pancreas, and liver. In the case of the lung this phenomenon is referred to as the 'gut-lung axis'. Recent studies have begun to explore and unveil the relationship between gut fungi and lung immunity in diseases such as asthma and lung cancer, and lung infections caused by viruses, bacteria and fungi. In this review we will summarize the current, rapidly growing, literature describing the impact of the gut mycobiome on respiratory disease and infection.

Microbiome and mycobiome analyses in continuous positive airway pressure devices.

Objectives: Microorganisms are likely present in continuous positive airway pressure (CPAP) devices used daily. Considering the potential risk of infections among CPAP device users, here we aimed to compare the microbiomes in CPAP devices with those in nasal mucosal samples obtained from corresponding individuals using these devices. Methods: We conducted a prospective cohort study at tertiary medical institutes. Samples were collected from the tubes and filters of CPAP devices and the nasal mucosa of corresponding individuals using these devices. Microbiomes and mycobiomes were analyzed using 16S ribosomal RNA and internal transcribed spacer region sequencing. Results were compared according to the sampling site and usage duration for each patient. Results: Overall, 27 paired human nasal mucosa and CPAP samples were analyzed. Bacteria were present in 7 of 27 tubes (29.6%) and 22 of 27 filters (81.5%). Fungi were present in 2 of the 27 tubes (7.4%) and 16 of the 27 filters (59.3%). Actinobacteria and Firmicutes were the predominant phyla among all samples. Fungi were not detected in any of the nasal mucosal samples. However, Basidiomycota and Ascomycota were predominant in the CPAP filters and tube samples. No significant associations were identified among the results according to sampling site and usage duration. Conclusion: Bacteria or fungi can be detected to some extent in CPAP samples even if the CPAP usage period is short. The association between respiratory infections and these microbiomes or mycobiomes was not investigated. Further research might be required to determine the risk posed by CPAP devices as a microbial contamination source.

Contributions of Hanseniaspora species to Pinot Noir microbial terroir in Oregon's Willamette Valley wine region.

The apiculate yeast genus Hanseniaspora has appeared frequently in enological research for more than 100 years, mostly focused upon the species H. uvarum due to its notable capacity to cause spoilage. Recently, there has been increased research into the potential benefits of other Hanseniaspora species, such as H. vineae, in producing more complex wines. Furthermore, large-scale DNA sequencing-based (metabarcoding) vineyard ecology studies have suggested that Hanseniaspora species may not be evenly distributed. To address potential differences across geographical areas in Oregon, we sampled extensively from 12 vineyards within the Willamette Valley American Viticultural Area (AVA), across 2 sub-AVAs (Eola-Amity Hills and Yamhill-Carlton). Metabarcoding was then used to assess the contribution of Hanseniaspora to the grape berry fungal community and the impact of wine processing on diversity. While 6 of the 23 recognized Hanseniaspora species were present on Pinot Noir grapes in the Willamette Valley AVA, differences between vineyards were driven by the abundance of H. uvarum. Significant positive correlations between the amount of H. uvarum present in must and at cold soak, and then cold soak to early ferment were observed. While intuitive, it is worth noting that no prior studies have observed this across such a large number of grape samples from different vineyards. Our results provide clear evidence that the abundance of H. uvarum on grapes may be an important predictor of potential impacts on wine quality, particularly if performing cold soak, which acts as an enrichment step. IMPORTANCE: Hanseniaspora yeasts are frequently found in uninoculated wine fermentations, and depending upon the species present, their contributions to the wine may be positive or negative. We found that in Oregon's Willamette Valley, the most common species of Hanseniaspora in Pinot Noir vineyards was the known spoilage organism, H. uvarum. This species was one of the strongest contributors to differences in fungal communities between different vineyards and was enriched during typical Pinot Noir processing. These results support Hanseniaspora as an integral and functional component of vineyard "microbial terroir" within Oregon.

Leaf age structures phyllosphere microbial communities in the field and greenhouse.

The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.

Microscopic fungi on the corpse - Promising tool requiring further research.

Forensic microbiology is a relatively new area of forensic sciences. It considers the potential of microorganisms to be used in criminal investigations. As most studies involve the role of bacteria in fields like post-mortem interval estimation, personal identification or geolocation, the data on the role of fungi is comparatively scarce. Forensic mycology involves the application of fungi and their structures in forensic cases. The aim of this review is the evaluation of the current state of knowledge on fungi associated with human cadavers and their possible role in estimating the time since death. In accordance with the available reports, we focused on the relation between microscopic fungi isolated from human corpses and the cadaver condition e.g., the stage of decomposition. We also emphasised the contrast between the reported methodologies and attempted to standardise research methods in forensic mycology from sample collection to its storage, mycological analysis and identification of the obtained fungal cultures. Moreover, the potential usage of microscopic fungi in criminal cases was discussed based on various case reports.

Mother trees of common ash (Fraxinus excelsior) disperse different sets of mycobiome through their seed wings.

OBJECTIVE: The endophytic mycobiome is present in all studied plant compartments, including fruits and seeds. Here, we studied the mycobiome of seed wings as they are transferred with seeds in common ash and tested whether the mycobiome differs among trees. To achieve this, we used ITS1-based amplicon sequencing and two genotypes of F. excelsior as a model to compare the mycobiome of mother trees and their wings. RESULTS: We compared the mycobiome of 57 seed wings to the seed stalks (57) collected from two genotypes of F. excelsior using three ramets of each genotype. Alpha diversity indices (ACE, Fisher and Observed OTUs) suggested a higher richness of the mycobiome associated with the seed wing than the seed stalk within each genotype. However, there were neither significant differences in Shannon diversity between the mycobiomes from the two tissue types nor the two genotypes. PERMANOVA revealed significant differences in the mycobiome composition between tissue types (P < 0.001). It also showed a significant difference between seed wings (P = 0.04), but not between seed stalks of the two genotypes. Our results suggest that Fraxinus excelsior mother trees disperse different sets of mycobiomes with their seed wings, which may be important for germination and seedling establishment-especially in the light of ash dieback.

Synthesis of current pediatric urinary microbiome research.

The human urinary bladder hosts a complex microbial community of low biomass referred to as the urobiome. While the composition of the urobiome has been investigated in adults for over a decade now, only a few studies have considered the presence and composition of the urobiome in children. It is critical to explore how the urobiome develops throughout the life span and how it changes in the presence of various health conditions. Therefore, we set to review the available data on pediatric urobiome composition and its development with age and disease. In addition, we focused on identifying and reporting specific gaps in our knowledge of the pediatric urobiome that we hope will be addressed by future studies in this swiftly developing field with fast-improving methods and consensus.

Metagenomics reveals unique gut mycobiome biomarkers in psoriasis.

PURPOSE: In present, the diagnosis of psoriasis is mainly based on the patient's typical clinical manifestations, dermoscopy and skin biopsy, and unlike other immune diseases, psoriasis lacks specific indicators in the blood. Therefore, we are required to search novel biomarkers for the diagnosis of psoriasis. METHODS: In this study, we analyzed the composition and the differences of intestinal fungal communities composition between psoriasis patients and healthy individuals in order to find the intestinal fungal communities associated with the diagnosis of psoriasis. We built a machine learning model and identified potential microbial markers for the diagnosis of psoriasis. RESULTS: The results of AUROC (area under ROC) showed that Aspergillus puulaauensis (AUROC = 0.779), Kazachstania africana (AUROC = 0.750) and Torulaspora delbrueckii (AUROC = 0.745) had high predictive ability (AUROC > 0.7) for predicting psoriasis, While Fusarium keratoplasticum (AUROC = 0.670) was relatively lower (AUROC < 0.7). CONCLUSION: The strategy based on the prediction of intestinal fungal communities provides a new idea for the diagnosis of psoriasis and is expected to become an auxiliary diagnostic method for psoriasis.