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Le mycobiome humain, variable selon sa localisation dans le corps, reste une entité faible au regard des autres composants du microbiome. Pourtant il semble jouer un rôle important en santé, notamment comme activateur de l'inflammation et de l'immunité. Il se constitue dès la naissance et peut varier en fonction du mode d'accouchement et de l'alimentation du nourrisson. Le mycobiome varie ensuite au cours de la vie en fonction de nombreux facteurs, dont l'alimentation, l'âge, le sexe, ou les différents traitements. Dans le poumon, comme dans le tube digestif, le mycobiome présente une grande variabilité intra-individuelle et se modifie en fonction de l'exposome alimentaire ou aérien. Le core mycobiome pulmonaire ou digestif est majoritairement composé de levures de type Candida (Saccharomycotina) et de Malassezia spp. Des dysbioses fongiques ont été décrites dans plusieurs pathologies, en particulier des maladies inflammatoires chroniques, mais aussi des cancers ou des maladies infectieuses non fongiques. Les Candida spp., acteurs du mycobiome, semblent avoir un rôle pro-inflammatoire ou même favoriser la tumorogenèse. Cette revue synthétise les connaissances actuelles sur le mycobiome de différents sites anatomiques et leur rôle dans la santé humaine. La connaissance du mycobiome du sujet sain permettra, à terme, de rechercher les dysbioses fongiques et leurs facteurs diagnostiques ou pronostiques. The human mycobiome, which varies according to its location, remains a small entity compared with the other components of the microbiome. It appears to play an important role in health, notably as an activator of inflammation and immunity. The mycobiome is formed at birth and can vary according to delivery mode and the infant's diet. Throughout life, the mycobiome varies depending on a number of factors, including diet, age, sex and treatments. In the lung, as in the digestive tract, the mycobiome shows great intra-individual variability and changes according to the dietary or airborne exposome. The pulmonary or digestive "core mycobiome" is mainly composed of Candida-type yeasts (Saccharomycotina) and Malassezia spp. Fungal dysbiosis has been described in several pathologies, in particular chronic inflammatory diseases, but also cancers and non-fungal infectious diseases. Candida spp., which are involved in mycobiome, appear to play a pro-inflammatory role or even promote tumorigenesis. This review summarizes current knowledge of the mycobiome at different anatomical sites and its role in human health. Knowledge of the mycobiome in healthy subjects will eventually enable us to investigate fungal dysbiosis and its diagnostic or prognostic factors. [ABSTRACT FROM AUTHOR]

Fungi have a well-established role in medicine. Herein, we describe the fungal profile and abundance in the gut of healthy Saudi children. Fecal samples from a random sample of 20 school-age Saudi children were collected, stored at −80 °C, and dispatched to the laboratory in the USA where fungal DNAs were isolated and shotgun metagenomic sequencing was performed. Abundance was presented as average percentage of fungal taxa. The median age of the participants was 12.5 years (range: 7–16 years), and 35 % were male. Ascomycota were the most abundant phyla and Eurotiomycetes, Saccharomycetes, were the most abundant class. The average abundance of fungal genera were Histoplasma (36 %) and Saccharomyces (31 %). The most abundant species were Histoplasma capsulatum (36 %) and Saccharomyces pastorianus (23 %). Other less abundant but may be functionally important genera and species included Candida (2.6 %) and Saccharomycescerevisiae (8 %). The profile and abundance of the gut fungi in healthy Saudi children reveals important differences compared to Western literature. Accordingly, this report represents a more appropriate reference than Western data to use as controls for regional studies aiming to identify fungi associated with disease. [ABSTRACT FROM AUTHOR]

Atopic diseases are characterized by type 2 inflammation, with high levels of allergen-specific T H 2 cell immune responses and elevated production of IgE. These common disorders have increased in incidence around the world, which is partly explained by detrimental disturbances to the early-life intestinal microbiome. Although most studies have focused exclusively on bacterial members of the microbiome, intestinal fungi have started to be recognized for their impact on host immune development and atopy pathogenesis. From this perspective, we review recent findings demonstrating the strong interactions between members of the mycobiome and the host immune system early in life, leading to immune tolerance during eubiosis or inducing sensitization and overt T H 2 cell responses during dysbiosis. Current evidence places intestinal fungi as central players in the development of allergic diseases and potential targets for atopy prevention and treatments. [ABSTRACT FROM AUTHOR]

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Candida auris and Candida albicans can result in invasive fungal diseases. And yet, these species can stably and asymptomatically colonize human skin and gastrointestinal tracts. To consider these disparate microbial lifestyles, we first review factors shown to influence the underlying microbiome. Structured by the damage response framework, we then consider the molecular mechanisms deployed by C. albicans to switch between commensal and pathogenic lifestyles. Next, we explore this framework with C. auris to highlight how host physiology, immunity, and/or antibiotic receipt are associated with progression from colonization to infection. While treatment with antibiotics increases the risk that an individual will succumb to invasive candidiasis, the underlying mechanisms remain unclear. Here, we describe several hypotheses that may explain this phenomenon. We conclude by highlighting future directions integrating genomics with immunology to advance our understanding of invasive candidiasis and human fungal disease. In this review, Proctor and colleagues spotlight two fungal pathogens— Candida auris and Candida albicans —named by the World Health Organization as urgent health threats. They explore the role of the microbiome, host physiology, host immunity, and antibiotics in modulating switches between commensalism, pathogenesis, and infection in Candida species. [ABSTRACT FROM AUTHOR]

Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections. [ABSTRACT FROM AUTHOR]

Contemporary research has increasingly explored the clinical applicability of next-generation DNA sequencing (NGS) technologies in veterinary medicine, which has provided new and practical opportunities for rabbit otitis externa clinical interventions. The objectives of this study were to characterize the normal external ear canal microbiome of clinically healthy rabbits compared to otitis externa presenting rabbits, and to assess the diagnostic viability of NGS in aural veterinary medicine. Swabs from the external ear canal of 34 clinically healthy rabbits and 16 rabbits diagnosed with otitis externa were collected. Alongside bioinformatic analysis, library preparation was performed targeting the V1-V3 region of the 16S rRNA bacterial gene and the ITS-2 region for fungal DNA analysis. In the clinically healthy group, the bacterial species with the highest relative abundances were an uncharacterized Phytoplasma from the family Acholeplasmataceae (8.74%) and Staphylococcus epidermidis (5.56%), while in the otitis group the species with the highest relative abundances were Staphylococcus aureus (12.59%), Corynebacterium lactis (9.27%), and Corynebacterium mastitidis (7.92%). Fungal species with the highest relative abundances in the healthy group were a species from the genus Cladosporium (14.46%), while in the otitis externa group the fungal species with the highest relative abundances were a species from the genus Cladosporium (9.89%) and Malassezia restricta (4.76%). Additionally, there was a significantly higher number of different bacterial and fungal species in the clinically healthy group compared to the otitis group (P = 0.00 and P = 0.00, respectively). This study provided evidence that the rabbit aural microbiome profile is distinctly different between a clinically healthy and an otitis state. It also highlighted new bacterial and fungal organisms of note in rabbits diagnosed with otitis externa compared to those previously thought to be the primary disease-causing organisms. Understanding the microbial population dynamics in the rabbit aural microbiome is particularly critical for helping clinicians recognize, prevent, or revert the progression of otitis. [ABSTRACT FROM AUTHOR]

The tumor microbiome of patients with pancreas ductal adenocarcinoma (PDAC) includes bacteria normally present in the upper gastrointestinal tract. If the predominant source of intratumoral bacteria in patients with PDAC is retrograde migration from the duodenum, duodenal fluid could be a representative biospecimen for determining microbiome profiles of patients with PDAC or at risk of developing PDAC. We performed a case-control study comparing bacterial and fungal (16S and 18S rRNA) profiles of secretin-stimulated duodenal fluid collections from 308 patients undergoing duodenal endoscopy including 134 normal pancreas control subjects, 98 patients with pancreatic cyst(s) and 74 patients with PDAC. Alterations in duodenal fluid microbiomes with diminished alpha diversity were significantly associated with age >70 and proton pump inhibitor use. Patients with PDAC had significantly decreased duodenal microbial alpha diversity compared with age-matched control subjects with normal pancreata and those with pancreatic cyst(s). There was evidence of enrichment of Bifidobacterium genera in the duodenal fluid of patients with PDAC compared with control subjects and those with pancreatic cyst(s). There were also enrichment of duodenal fluid Fusobacteria and Rothia bacteria among patients with PDAC with short-term survival. Duodenal fluid microbiome profiles were not significantly different between control subjects and patients with pancreatic cyst(s). Patients with PDAC have alterations in their duodenal fluid microbiome profiles compared with patients with pancreatic cysts and those with normal pancreata. ClinicalTrials.gov , Number: NCT02000089 [ABSTRACT FROM AUTHOR]

The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease. [ABSTRACT FROM AUTHOR]

We investigated the wood fungal community composition in stems of living Norway spruce (Picea abies (L.) Karst.) trees in 20–40 year-old forest stands from Latvia that differed in recent management history (stands with or without thinning) and former land use (former agricultural or former forest lands). Fungal internal transcribed spacer (ITS2) amplicons of DNA extracted from wood were sequenced to assess wood fungal communities. Alternaria, Ascocoryne, Didymella, Heterobasidion, Ophiostoma, Orbilia, Pesotum, Phoma and Pseudocercosporella were the dominant wood pathogen and wood saprotroph genera in the analysed samples. PERMANOVA analysis identified some differences in fungal communities among site types analysed (p < 0.001); tree height and presence/absence of rot in the wood samples (mainly Heterobasidion rot) significantly influenced fungal community composition (p < 0.001). Significant negative co-occurrence (p < 0.05) was observed between Heterobasidion and Ascocoryne genera indicating the differing wood colonizing niches of these taxa. Both stand level factors, such as management history and former land use, and tree level parameters are significant for wood inhabiting fungal communities of living spruces. [ABSTRACT FROM AUTHOR]

Fungal endophytes of plants are ubiquitous and important to host plant health. Wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across the Fushan forest dynamics plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Despite this, host tree species was an important predictor of mycobiome community-composition. Within a single common tree species, "core" mycobiomes were characterized using co-occurrence analysis. The spatial co-occurrence patterns of these few species of fungal endophytes appear to explain the strong host effect. For wood endophytes, a consistent core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, "gradient" model of the core microbiome, changing across the topography and distance of the study. [ABSTRACT FROM AUTHOR]

Abstract Insufficient reference database coverage is a widely recognized limitation of molecular ecology approaches which are reliant on database matches for assignment of function or identity. Here, we use data from 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spacer (ITS) region of fungal rDNA to identify substrates and geographic areas whose underrepresentation in the available reference databases could have meaningful impact on our ability to draw ecological conclusions. A total of 14 different substrates were investigated. Database representation was particularly poor for the fungal communities found in aquatic (freshwater and marine) and soil ecosystems. Aquatic ecosystems are identified as priority targets for the recovery of novel fungal lineages. A subset of the data representing soil samples with global distribution were used to identify geographic locations and terrestrial biomes with poor database representation. Database coverage was especially poor in tropical, subtropical, and Antarctic latitudes, and the Amazon, Southeast Asia, Australasia, and the Indian subcontinent are identified as priority areas for improving database coverage in fungi. Highlights • Geographic and substrate database biases identified using environmental sequences. • Soil and aquatic fungi are particularly underrepresented in the reference databases. • Aquatic ecosystems are priority targets for the recovery of novel fungal lineages. • Database coverage was especially poor in (sub)tropical and Antarctic latitudes. [ABSTRACT FROM AUTHOR]

Abstract Nothing is sterile. Insects, plants, and fungi, highly speciose groups of organisms, conceal a vast fungal biodiversity. An approximation of the total number of fungal species on Earth remains an elusive goal, but estimates should include fungal species hidden in associations with other organisms. Some specific roles have been discovered for the fungi hidden within other life forms, including contributions to nutrition, detoxification of foodstuffs, and production of volatile organic compounds. Fungi rely on associates for dispersal to fresh habitats and, under some conditions, provide them with competitive advantages. New methods are available to discover microscopic fungi that previously have been overlooked. In fungal conservation efforts, it is essential not only to discover hidden fungi but also to determine if they are rare or actually endangered. [ABSTRACT FROM AUTHOR]

Fungi are increasingly being recognized as common members of the microbiomes found on nearly all mucosal surfaces, and interest is growing in understanding how these organisms may contribute to health and disease. In this review, we investigate recent developments in our understanding of the fungal microbiota or “mycobiota” including challenges faced in characterizing it, where these organisms are found, their diversity, and how they interact with host immunity. Growing evidence indicates that, like the bacterial microbiota, the fungal microbiota is often altered in disease states, and increasingly studies are being designed to probe the functional consequences of such fungal dysbiosis on health and disease. [ABSTRACT FROM AUTHOR]

Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living “organ” that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies. [ABSTRACT FROM AUTHOR]

Alcohol-associated liver disease is accompanied by intestinal mycobiome dysbiosis, yet the impacts on liver disease are unclear. We demonstrate that Candida albicans -specific T helper 17 (Th17) cells are increased in circulation and present in the liver of patients with alcohol-associated liver disease. Chronic ethanol administration in mice causes migration of Candida albicans (C. albicans)-reactive Th17 cells from the intestine to the liver. The antifungal agent nystatin decreased C. albicans- specific Th17 cells in the liver and reduced ethanol-induced liver disease in mice. Transgenic mice expressing T cell receptors (TCRs) reactive to Candida antigens developed more severe ethanol-induced liver disease than transgene-negative littermates. Adoptively transferring Candida -specific TCR transgenic T cells or polyclonal C. albicans -primed T cells exacerbated ethanol-induced liver disease in wild-type mice. Interleukin-17 (IL-17) receptor A signaling in Kupffer cells was required for the effects of polyclonal C. albicans -primed T cells. Our findings indicate that ethanol increases C. albicans -specific Th17 cells, which contribute to alcohol-associated liver disease. [Display omitted] • Alcohol increases intestinal C. albicans -specific Th17 cells that migrate to the liver • An antifungal agent reduces C. albicans -specific Th17 cells in the liver • Adoptive transfer of C. albicans -specific Th17 cells promotes liver disease • C. albicans -specific Th17 cells promote liver disease via IL17ra on Kupffer cells How fungal dysbiosis contributes to alcohol-associated liver disease is unclear. Zeng et al. find that C. albicans -specific Th17 cells increase in the blood and liver of patients with alcohol-associated liver disease. In mice, C. albicans -specific Th17 cells migrate from the intestine to the liver, where they contribute to ethanol-induced liver disease. [ABSTRACT FROM AUTHOR]

Sapwood comprises much above-ground forest biomass, but its mycobiome in living trees is largely unknown. Here, we characterize the endophytic fungal communities of the functional sapwood of young and mature living beech trees (Fagus sylvatica) at multiple scales, from within individual trees to woodland sites across the southern United Kingdom. Fungal community composition was determined using both culture-based and molecular approaches across two loci. Wood decay fungi, including those that cause heart rot, were detected in approximately 80% of all samples. Fungal community composition differed according to the survey approach (high throughput sequencing vs. isolation of fungi into culture) and between geographic location and individual trees, but no significant patterns were detected at different heights in individual trees or around their circumferences. ITS and LSU sequencing detected more distinct taxa than culturing. However, LSU primers yielded more OTUs than did ITS primers, though both identified unique OTUs. This highlights the importance of multiple survey approaches, including multiple primer pairs, for better characterisation of communities and confidence in results of endophyte studies. [ABSTRACT FROM AUTHOR]

Wood-decay fungi soften wood, putatively providing opportunities for woodpeckers to excavate an otherwise hard substrate, yet the fungal community composition in tree cavities and the specificity of these relationships is largely unknown. We used high-throughput amplicon sequencing of the fungal ITS2 region to examine the fungal communities associated with acorn woodpeckers (Melanerpes formicivorus) and their cavities in mature valley oak (Quercus lobata) and blue oak (Q. douglasii) trees in an oak savannah of central coastal California, USA. Acorn woodpeckers and their excavations harbored over 1500 fungal taxa, including more than 100 putative wood-decay fungi. The fungal communities found on the birds were more similar to those found in excavated cavities than those found in trees without excavated holes. These results suggest that symbiotic associations between acorn woodpeckers and fungi are highly diverse, with low specificity. Symbiotic associations between cavity-excavators and fungi are likely more common and widespread than previously thought. [ABSTRACT FROM AUTHOR]

Résumé Le mycobiote se réfère à la composante fongique du microbiote vivant au sein d’un environnement donné. Le mycobiote humain fait donc partie du microbiote humain, au même titre que les bactéries. Malgré son importance, il reste peu étudié. De nouvelles approches indépendantes de la culture, comme les méthodes de séquençage à haut débit, développées ces dernières années, permettent d’aborder la diversité fongique dans les microbiotes par le biais de leur contenu génique (ou mycobiome). Les quelques études déjà publiées dans la littérature montrent que les différentes parties du corps humain abritent des populations fongiques spécifiques et que certains profils de mycobiome sont associés à différentes pathologies. En interaction avec d’autres biomes, ainsi qu’avec l’hôte, le mycobiome joue probablement un rôle important dans la santé humaine. Summary The mycobiota refers to the fungal component of the overall microbiota inhabiting a specific ecosystem. The human mycobiota is thus part of the human microbiota along with bacteria, archeobacteria, protozoa and viruses. Despite its importance, it has remained understudied. However, with to the development of new culture-independent approaches over the past decade, which allow the study of the mycobiota through the characterization of its genes content (= mycobiome), our knowledge on the fungal diversity in the human body has broadened. The studies published so far have shown that specific fungal populations inhabit different body sites and that specific mycobiome pattern might be associated with particular diseases. Moreover, through its interaction with other components of the microbiota, as well as with the host, the mycobiota might play an important role in human health. [ABSTRACT FROM AUTHOR]

Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium- driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants. [Display omitted] • Multi-strain regimen accelerates microbiome maturation in extremely premature infants • Bifidobacterium strains can colonize several months after administration ceases • Bifidobacteria act as ecosystem engineers for a more mature and stable community • Microbiome maturation is associated with a favorable metabolic and immune gut milieu The effects of probiotics on premature infants are not well understood. In a randomized intervention trial, Samara et al. show that a multi-strain mix accelerated microbiome maturation to resemble that of full-term infants and improved the metabolic and immune parameters, highlighting the critical ecological role of these species in early-life microbiome. [ABSTRACT FROM AUTHOR]

Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Nonbacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the nonbacterial and nonarchaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease. [Copyright &y& Elsevier]

• Soil fungal communities (SFC) were determined by DNA barcoding-Illumina sequencing. • SFC differ among beech, conifer and mixed beech conifer stands. • Relative abundance of conifers, region, and soil chemistry shape SFC. • The guilds of saprotrophic fungi increased and mycorrhizas were unaffected by conifers. • Phylogenetically related fungal taxa show variable responses to site conditions. Soil fungi, especially the functional guilds of saprotrophs and symbiotrophs, play a central role in ecosystem processes such as decomposition and plant nutrient acquisition. Fungal communities are influenced by soil properties and management strategies such as tree species selection. Yet, the implications of the enrichment of temperate forests consisting of tree species in their native range with non-native tree species on soil fungal diversity and their functional groups are unknown. Here, we studied fungal communities in 40 plots (2500 m2 size per plot) located in two regions differing in site conditions (nutrient content, soil moisture and climate) in forests composed of European beech, spruce and Douglas-fir (non-native) and mixtures of beech with either spruce or Douglas-fir. We hypothesized that fungal community structures are driven by soil properties and tree species composition, generally resulting in higher fungal diversity in mixed than in mono-specific forests. We further hypothesized that Douglas-fir has a negative effect on ectomycorrhizal fungal species richness compared to native species, whereas saprotrophic fungal richness is unaffected. Fungal DNA barcoding and dissimilarity analyses showed significant separation of fungal communities between nutrient-rich and nutrient-poor regions and among forest types. Mycorrhizal species richness did not vary with forest type, but the relative abundance of mycorrhizal species was lower in Douglas-fir and mixed beech-Douglas-fir forests than in spruce or beech-spruce mixture forests. Conifer forests contained higher relative abundances of saprotrophic fungi than mono-specific beech forests. Among 16 abundant fungal orders in the soil, two containing saprotrophic fungi (Tremellales and Hymenochaetales) were enriched in conifer forests, regardless of site conditions and tree species mixture. The other fungal orders, including those dominated by mycorrhizal fungi (Russulales, Boletales, Atheliales and Cantharellales) showed variable patterns depending on site conditions and tree species. Our results show the impact of tree species composition and soil properties on soil fungi. The response of fungal guilds and taxa to forest types and soil properties can potentially influence nutrient fluxes. [ABSTRACT FROM AUTHOR]

Social spiders of the species Stegodyphus dumicola live in communal nests with hundreds of individuals and are characterized by extremely low species-wide genetic diversity. The lack of genetic diversity in combination with group living imposes a potential threat for infection by pathogens. We therefore proposed that specific microbial symbionts inhabiting the spider nests may provide antimicrobial defense. To compare the bacterial and fungal diversity in 17 nests from three different locations in Namibia, we used 16S rRNA gene and internal transcribed spacer (ITS2) sequencing. The nest microbiomes differed between geographically distinct spider populations and appeared largely determined by the local environment. Nevertheless, we identified a core microbiome consisting of four bacterial genera (Curtobacterium, Modestobacter, Sphingomonas, Massilia) and four fungal genera (Aureobasidium, Didymella, Alternaria, Ascochyta), which likely are selected from surrounding soil and plants by the nest environment. We did not find indications for a strain- or species-specific symbiosis in the nests. Isolation of bacteria and fungi from nest material retrieved a few bacterial strains with antimicrobial activity but a number of antimicrobial fungi, including members of the fungal core microbiome. The significance of antimicrobial taxa in the nest microbiome for host protection remains to be shown. [ABSTRACT FROM AUTHOR]

The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters. The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma. [Display omitted] [ABSTRACT FROM AUTHOR]

Despite of known pathogenic potential of human mycobiome in initiation and progression of oral disorders, it is poorly characterized and understudied due to its small number in oral cavity. In the present study, salivary mycobiome of three postpartum females along with one healthy non-pregnant female was investigated by targeting ITS region. A total of 55 genera and 92 species were detected with predominant genera: Candida (12.2%) followed by Saccharomyces (9.27%), Phialosimplex (9.19%), Termitomyces (6.96%), Penicillium (6.85%), Aspergillus (6.56%), Olpidium (5.15%), Cochliobolus (4.78%), Malassezia (4.61%), Neurospora (4.3%), and Cristinia (3.04%) in all samples. Diversity increase was observed in postpartum group as compared to non-pregnant female. Stachybotrys, Geotrichum, Talaromyces, Leucosporidium, Acremonium, Wallemia, Eupenicillium, Septoria, Zymoseptoria, Coniosporium, Phialophora , and Mycosphaerella were genera detected only in postpartum group. Postpartum female with gingivitis and dental caries showed greater abundance of genus Saccharomyces, Phialosimplex, Candida, Olpidium, Cochliobolus, Malaseezia, Hyphodontia, Debaryomyces, Mrakia, and Nakaseomyces as compared to those postpartum females with good oral health. Among postpartum group female with oral health issues as well as who had preterm low weight birth (PLWB), showed reduced richness, evenness with elevated levels of Saccharomyces, Candida, Hyphodontia and Malassezia compared to the female having full term birth (FTB). These findings showed that, pregnancy with or without oral health issues is associated with oral microbial diversity change and there might be an association of changing fungal diversity with adverse pregnancy outcomes (APOs) like pre-term birth (PTB) and low weight birth (LWB). [ABSTRACT FROM AUTHOR]

Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity, and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association with host factors, environmental factors, and diets. Using shotgun metagenomic sequencing, we profiled and compared the fecal mycobiome of 942 healthy individuals across different geographic regions in China (Hong Kong and Yunnan), spanning 6 ethnicities: Han, Zang, Bai, Hani, Dai, and Miao (including both urban and rural residents of each ethnicity). In parallel to fecal sampling, we collected participant metadata (environmental exposure, bowel habits, anthropometrics, and medication), diet, and clinical blood measurement results (a total of 118 variables) and investigated their impact on the gut mycobiome variation in humans. The human gut mycobiome was highly variable across populations. Urbanization-related factors had the strongest impact on gut mycobiome variation, followed by geography, dietary habit, and ethnicity. The Hong Kong population (highly urbanized) had a significantly lower fungal richness compared with Yunnan population. Saccharomyces cerevisiae was highly enriched in urban compared with rural populations and showed significant inverse correlations with liver pathology–associated blood parameters, including aspartate transaminase, alanine transaminase, gamma-glutamyltransferase, and direct bilirubin. Candida dubliniensis , which was decreased in urban relative to rural populations, showed correlations with host metabolism-related parameters in blood, including a positive correlation with fasting high-density lipoprotein cholesterol levels and a negative correlation with fasting glucose levels. The fungal-blood parameter correlations were highly geography- and ethnicity-specific. Food choices had differential influences on gut mycobiome and bacterial microbiome, where taxa from the same genus tended to be coregulated by food and thereby cobloom. Ethnicity-specific fungal signatures were associated with distinct habitual foods in each ethnic group. Our data highlight, for the first time to our knowledge, that geography, urbanization, ethnicity, and habitual diet play an important role in shaping the gut mycobiome composition. Gut fungal configurations in combination with population characteristics (such as residing region, ethnicity, diet, lifestyle) influence host metabolism and health. [ABSTRACT FROM AUTHOR]

Termites are important plant biomass decomposers. Their digestive activity typically relies on prokaryotes and protozoa present in their guts. In some cases, such as in fungus-growing termites, digestion also relies on ectosymbiosis with specific fungal taxa. To date, the mycobiome of termites has yet to be investigated in detail. We evaluated the specificity of whole-termite associated fungal communities in three wood-feeding termite species. We showed that the whole-termite fungal community spectra are stable over diverse environments, regardless of the host species, and differ markedly from the wood in which they nest. The core mycobiome is similar to that found in other ecologically related insects and consists of a narrow spectrum of common filamentous fungi and yeasts, known for their stress tolerance and their ability to decompose plant biomass. The observed patterns suggest that a number of fungal strains may have a symbiotic relationship with termites, and our results set the stage for future investigations into the interactions between fungi, termites, and their other gut microbiota. Image 1 • Termite body associated mycobiome is systematically studied for the first time. • Whole termite bodies were used as a proxy for the intestinal mycobiota study. • Body associated fungal communities differ from the ambient environment. • Body associated communities are stable over variable habitats and termite species. • This is a first sign that termites have a symbiosis with intestinal fungi. [ABSTRACT FROM AUTHOR]

Summary Inflammatory bowel disease (IBD) is characterized by alterations in the intestinal microbiota and altered immune responses to gut microbiota. Evidence is accumulating that IBD is influenced by not only commensal bacteria but also commensal fungi. We characterized fungi directly associated with the intestinal mucosa in healthy people and Crohn's disease patients and identified fungi specifically abundant in patients. One of these, the common skin resident fungus Malassezia restricta , is also linked to the presence of an IBD-associated polymorphism in the gene for CARD9, a signaling adaptor important for anti-fungal defense. M. restricta elicits innate inflammatory responses largely through CARD9 and is recognized by Crohn's disease patient anti-fungal antibodies. This yeast elicits strong inflammatory cytokine production from innate cells harboring the IBD-linked polymorphism in CARD9 and exacerbates colitis via CARD9 in mouse models of disease. Collectively, these results suggest that targeting specific commensal fungi may be a therapeutic strategy for IBD. Graphical Abstract Highlights • M. restricta is associated with the colonic mucosa in Crohn's disease (CD) patients • M. restricta exacerbates colitis in wild-type and gnotobiotic mice • M. restricta is found in CD patients with a disease-linked polymorphism in CARD9 • Malassezia -exacerbated colitis in mice requires signaling via CARD9 Limon et al. surveyed intestinal wall-associated fungi in patients with Crohn's disease (CD) and healthy controls and found a common commensal skin yeast called Malassezia , preferentially in CD patients. Malassezia exacerbates colitis in mouse models through mechanisms requiring CARD9, a signaling protein involved in anti-fungal immunity. [ABSTRACT FROM AUTHOR]

Summary Sensing of the gut microbiota, including fungi, regulates mucosal immunity. Whether fungal sensing in the gut can influence immunity at other body sites is unknown. Here we show that fluconazole-induced gut fungal dysbiosis has persistent effects on allergic airway disease in a house dust mite challenge model. Mice with a defined community of bacteria, but lacking intestinal fungi were not susceptible to fluconazole-induced dysbiosis, while colonization with a fungal mixture recapitulated the detrimental effects. Gut-resident mononuclear phagocytes (MNPs) expressing the fractalkine receptor CX3CR1 were essential for the effect of gut fungal dysbiosis on peripheral immunity. Depletion of CX3CR1+ MNPs or selective inhibition of Syk signaling downstream of fungal sensing in these cells ameliorated lung allergy. These results indicate that disruption of intestinal fungal communities can have persistent effects on peripheral immunity and aggravate disease severity through fungal sensing by gut-resident CX3CR1+ MNPs. Graphical Abstract Highlights • Fungal dysbiosis persistently aggravates allergic airway disease (AAD) in mice • Gut colonization by commensal fungi is both required and sufficient to aggravate AAD • Intestinal CX3CR1+ mononuclear phagocytes (MNPs) are essential for the effects • Inhibition of Syk-mediated fungal sensing in intestinal CX3CR1+ MNPs ameliorates AAD How mycobiota influence immunity in gut distal sites is not well understood. Li et al. developed protocols for gut-targeted depletion of phagocytes and mycobiota-free mice to investigate the influence of fungi on gut-lung crosstalk. They reveal that intestinal phagocytes sense fungal dysbiosis and mediate gut-lung-directed immunity to aggravate allergic airway disease. [ABSTRACT FROM AUTHOR]

Background Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. Objective We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting. Methods We conducted a case-control study nested within a birth cohort from rural Ecuador in which we identified 27 children with atopic wheeze and 70 healthy control subjects at 5 years of age. We analyzed bacterial and eukaryotic gut microbiota in stool samples collected at 3 months of age using 16S and 18S sequencing. Bacterial metagenomes were predicted from 16S rRNA data by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and categorized by function with Kyoto Encyclopedia of Genes and Genomes ontology. Concentrations of fecal short-chain fatty acids were determined by using gas chromatography. Results As previously observed in Canadian infants, microbial dysbiosis at 3 months of age was associated with later development of atopic wheeze. However, the dysbiosis in Ecuadorian babies involved different bacterial taxa, was more pronounced, and also involved several fungal taxa. Predicted metagenomic analysis emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. Levels of the fecal short-chain fatty acids acetate and caproate were reduced and increased, respectively, in the 3-month stool samples of children who went on to have atopic wheeze. Conclusions Our findings support the importance of fungal and bacterial microbiota during the first 100 days of life on the development of atopic wheeze and provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy. [ABSTRACT FROM AUTHOR]