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The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing amongst consortium members, which includes collaborators in academia and industry. The 6th Annual TSMC Symposium was a hybrid meeting held in Fairlee, Vermont on 27–28 September 2022 with presentations and discussions centered on microbiome-related topics within seven broad thematic areas: (1) Human Microbiomes: Stress Response; (2) Microbiome Analysis & Surveillance; (3) Human Microbiomes Enablers & Engineering; (4) Human Microbiomes: Countermeasures; (5) Human Microbiomes Discovery - Earth & Space; (6) Environmental Micro & Myco-biome; and (7) Environmental Microbiome Analysis & Engineering. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the activities and outcomes from the 6th annual TSMC symposium. [ABSTRACT FROM AUTHOR]

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The microorganisms inhabiting our gastrointestinal tract are critical for human health. Chronic heavy alcohol use can modulate the composition and function of the gut microbiota, thereby exacerbating end‐organ damage via the gut–brain axis and the gut–liver axis. In this review, we summarize the bacterial, fungal, and viral gut microbial compositional changes associated with alcohol use and alcohol‐associated liver disease and discuss the mechanisms of action by which gut dysbiosis reinforces alcohol use behavior and liver inflammation and injury. We also highlight important pre‐clinical and clinical trials that target gut microbial‐specific mechanisms for the treatment of alcohol use disorder and alcohol‐associated liver disease. [ABSTRACT FROM AUTHOR]

Accumulating evidence suggests that the upper airway bacterial microbiota is implicated in asthma inception, severity, and exacerbation. Unlike bacterial microbiota, the role of the upper airway fungal microbiome (mycobiome) in asthma control is poorly understood. What are the upper airway fungal colonization patterns among children with asthma and their relationship with subsequent loss of asthma control and exacerbation of asthma? The study was coupled with the Step Up Yellow Zone Inhaled Corticosteroids to Prevent Exacerbations (ClinicalTrials.gov Identifier: NCT02066129) clinical trial. The upper airway mycobiome was investigated using Internal transcribed spacer 1 (ITS1) sequencing of nasal blow samples collected from children with asthma when asthma was well controlled (baseline, n = 194) and during early signs of loss of asthma control (yellow zone [YZ], n = 107). At baseline, 499 fungal genera were detected in the upper airway samples, with two commensal fungal species, Malassezia globosa and Malassezia restricta , being most dominant. The relative abundance of Malassezia species varies by age, BMI, and race. Higher relative abundance of M globosa at baseline was associated with lower risk of future YZ episodes (P =.038) and longer time to development of first YZ episode (P =.022). Higher relative abundance of M globosa at YZ episode was associated with lower risk of progression from YZ episode to severe asthma exacerbation (P =.04). The upper airway mycobiome underwent significant changes from baseline to YZ episode, and increased fungal diversity was correlated highly with increased bacterial diversity (ρ = 0.41). The upper airway commensal mycobiome is associated with future asthma control. This work highlights the importance of the mycobiota in asthma control and may contribute to the development of fungi-based markers to predict asthma exacerbation. [Display omitted] [ABSTRACT FROM AUTHOR]

Intestinal fungi play an important role in the health-disease process. We observed that in liver diseases, fungal infections lead to high mortality. In this review, we were able to gather and evaluate the available scientific evidence on intestinal mycobiota and liver diseases. We searched PubMed and Embase, using a combination of several entry terms. Only studies in adults ≥ 18 years old with liver disease and published after 2010 were included. We observed that individuals with liver disease have an altered intestinal mycobioma, which accompanies the progression of these diseases. In cirrhotic patients, there are a high number of Candida sp. strains, especially Candida albicans. In early chronic liver disease, there is an increase in alpha diversity at the expense of Candida sp. and conversely, in advanced liver disease, there is a negative correlation between alpha diversity and model for end-stage liver disease score. On the other hand, patients with non-alcoholic fatty liver disease demonstrate greater diversity compared to controls. Our study concluded that the evidence on the subject is sparse, with few studies and a lack of standardization of outcome measures and reporting, and it was not possible to perform a meta-analysis capable of synthesizing relevant parameters of the human mycobiotic profile. However, certain fungal genera such as Candida play an important role in the context of liver disease and that adults with liver disease have a distinct gut mycobiotic profile from healthy controls. [ABSTRACT FROM AUTHOR]

Trichomoniasis, caused by Trichomonas vaginalis (TV), is the most common non-viral sexually transmitted infection (STI) worldwide, affecting over 174 million people annually and is frequently associated with reproductive co-morbidities. However, its detection can be time-consuming, subjective, and expensive for large cohort studies. This case–control study, conducted at the Mount Sinai Adolescent Health Center in New York City, involved 36 women with prevalent TV infections and 36 controls. The objective was to examine Internal Transcribed Spacer region-1 (ITS1) amplicon-derived communities for the detection of prevalent TV infections with the same precision as clinical microscopy and the independent amplification of the TV-specific TVK3/7 gene. DNA was isolated from clinician-collected cervicovaginal samples and amplified using ITS1 primers in a research laboratory. Results were compared to microscopic wet-mount TV detection of concurrently collected cervicovaginal samples and confirmed against TV-specific TVK3/7 gene PCR. The area under the receiver operating characteristics curve (AUC) for diagnosing TV using ITS1 communities was 0.92. ITS1 amplicons displayed an intra-class correlation coefficient (ICC) of 0.96 (95% CI: 0.93–0.98) compared to TVK3/7 PCR fragment testing. TV cases showed an increased risk of bacterial vaginosis (BV) compared to the TV-negative controls (OR = 8.67, 95% CI: 2.24–48.54, p-value = 0.0011), with no significant differences regarding genital yeast or chlamydia infections. This study presents a bioinformatics approach to ITS1 amplicon next-generation sequencing that is capable of detecting prevalent TV infections. This approach enables high-throughput testing for TV in stored DNA from large-scale epidemiological studies. [ABSTRACT FROM AUTHOR]

Agricultural intensification causes plant diversity loss and environmental homogenization, which may result in changes to plant-microbiome interactions mediating plant growth and stress tolerance. We hypothesized that foliar fungal microbiomes would depend on plant traits and environmental filters, constrained by neighboring vegetation expected to serve as a fungal source. Thus, we sampled foliar fungi from four crops (three annual and one perennial), four sites per crop, and three varieties per annual crop, across a 500-km expanse in North Carolina, USA and tested the role of host traits, environmental traits, and vegetative landcover on foliar fungal community structure. Crop species and site were major determinants of community structure, primarily due to differences in plant size and growing season. Site consistently explained 10× more variation in community structure than host variety across the annual crops. Finally, reduced natural vegetative cover surrounding farms was correlated with decreased fungal richness and more homogeneous microbiome assembly. Based on these results, we posit that foliar fungal assembly in crops results from host and environmental filters acting on inputs from the nearby vegetation. Future efforts at agricultural microbiome management must therefore consider landscape management and will require an improved understanding of how agricultural intensification alters microbial source pools. [ABSTRACT FROM AUTHOR]

The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID‐19). However, the oral fungal microbiota in COVID‐19 remains unclear. This article aims to characterize the oral mycobiome in COVID‐19 and recovered patients. Tongue coating specimens of 71 COVID‐19 patients, 36 suspected cases (SCs), 22 recovered COVID‐19 patients, 36 SCs who recovered, and 132 controls from Henan are collected and analyzed using internal transcribed spacer sequencing. The richness of oral fungi is increased in COVID‐19 versus controls, and beta diversity analysis reveals separate fungal communities for COVID‐19 and control. The ratio of Ascomycota and Basidiomycota is higher in COVID‐19, and the opportunistic pathogens, including the genera Candida, Saccharomyces, and Simplicillium, are increased in COVID‐19. The classifier based on two fungal biomarkers is constructed and can distinguish COVID‐19 patients from controls in the training, testing, and independent cohorts. Importantly, the classifier successfully diagnoses SCs with positive specific severe acute respiratory syndrome coronavirus 2 immunoglobulin G antibodies as COVID‐19 patients. The correlation between distinct fungi and bacteria in COVID‐19 and control groups is depicted. These data suggest that the oral mycobiome may play a role in COVID‐19. [ABSTRACT FROM AUTHOR]

Intensive development of phytopathogenic micromycetes in the agrocenoses of cultivated plants leads to significant crop losses, deterioration of its quality and reduction of plant productivity. Phytopathogens are a powerful factor in biological pollution of agroecosystems. The purpose of our study is to determine the number and species composition of micromycetes on the leaves of sunflower plants of Dushko and Oliver hybrids and winter wheat of Podolyanka and Skagen varieties in the agrocenoses of the Central Forest Steppe of Ukraine. Studies of the mycobiome of the leaves of sunflower plants have shown that the number of micromycetes is significantly influenced by the biological features of the investigated sunflower hybrids and their cultivation technologies. It was established that the number of phytopathogenic micromycetes on the vegetative organs of the investigated hybrids under the organic technology of sunflower cultivation was at the level of the traditional technology and varied between 14.6 and 19.9 thousand CFU/g of dry leaf. The species composition of micromycetes on the leaves of sunflower plants was determined and it was established that the dominant fungi are the following genera: Aspergillus P. Micheli ex Haller, Alternaria Nees, Penicillium Link; Fr, Fusarium Link and Cladosporium Link. They were characterized by a different frequency of occurrence during the growing season, which ranged from 15 to 70%. According to the results of the research of the mycobiome of the leaves of winter wheat plants, it was established that the number of micromycetes on plant leaves ranged from 0.9 to 3.8 thousand CFU/g of dry leaf and significantly depended on the cultivation technology and biological characteristics of plants of different breeding origins. Metabolites of Podolyanka winter wheat plants under conditions of both traditional and organic growing technology stimulated the development of micromycetes in the mycobiome of vegetative organs of plants. Metabolites of Skagen winter wheat plants under conditions of different cultivation technologies restrained the development of micromycetes at an ecologically safe level. The species composition of micromycetes on the vegetative organs of winter wheat plants was determined, and it was established that under the conditions of traditional growing technology, the dominant micromycetes were the species F. oxysporum, F. graminearum, and B. sorokiniana with a frequency of occurrence of 55 to 70%. And in the conditions of organic cultivation technology - F. oxysporum and T.viride, the frequency of which was 50%. Micromycetes of these genera are toxin-producing species that contaminate agricultural crops with mycotoxins, which poses a danger to animal and human health. [ABSTRACT FROM AUTHOR]

Bats can be affected by fungal pathogens such as Pseudogymnoascus destructans, the causative agent of the white-nose syndrome. Their body surface can also be colonized by fungal commensals or carry transient fungal species and participate in their dispersal. In this study, 114 bat specimens belonging to seven species were sampled from various locations in northern Belgium. Culture-based methods revealed an important mycological diversity, with a total of 209 different taxa out of the 418 isolates. Overall, a mean of 3.7 taxa per bat was recorded, but significant differences were observed between sampling sites and seasons. The mycobiomes were dominated by cosmopolitan and plant-associated species, in particular from the genera Cladosporium, Penicillium, and Aspergillus. Other species known to be related to bats or their environment, such as Apiotrichum otae, were also retrieved. Sampling of hibernacula indicated that diverse fungal species can inhabit these sites, including a yet undescribed Pseudogymnoascus species, distinct from Ps. destructans, namely, Ps. cavicola. [ABSTRACT FROM AUTHOR]

Both exposure to antibiotics at birth and delivery via Caesarean section influence the gut bacteriome's development in infants. Using 16S rRNA and internal transcribed spacer sequencing on the Ion Torrent platform, we employed network analysis to investigate the bacterial and fungal interkingdom relationships in the gut microbiome from birth to age 18 months in a prospective cohort study of 140 infants. The gut microbiome at ages six and 18 months revealed distinctive microbial interactions, including both positive and negative associations between bacterial and fungal genera in the gut ecosystem. Perinatal factors, delivery mode and intrapartum antibiotic exposure affected the associations between bacterial and fungal species. In infants exposed and unexposed to perinatal antibiotics, the gut microbiome formed distinct networks for the bacteriome and mycobiome. The fungi Saccharomyces, Trichosporon, Pezoloma, Cystofilobasidium, Rigidoporus and Fomitopsis were strongly associated with exposure to antibiotics at birth. Hyaloscypha, Trichosporon, Fomitopsis and Vishniacozyma were strongly associated with the control group that was not exposed to antibiotics. Five distinct networks were formed according to delivery mode. The present study confirms that bacteria and fungi clearly interact in the infant gut ecosystem. Furthermore, perinatal factors appear to influence the relationships between bacteria and fungi in the developing gut microbiome. [ABSTRACT FROM AUTHOR]

Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices. [ABSTRACT FROM AUTHOR]

There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or modify the bacterial composition via interkingdom interactions. Although several studies have demonstrated alterations in the fecal fungal microbiota composition in IBD, there is a wide variation in the mycobiome in different populations, with no definite pattern that can define the mycobiome in IBD having yet been identified. Recent work has suggested that characterizing the fecal fungal composition may influence therapeutic decisions and help to predict outcomes in a subset of IBD patients. In this study, we review the current literature on the emerging role of the fecal mycobiome as a potential tool for precision medicine in IBD. [ABSTRACT FROM AUTHOR]

The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a potential cause of disease, as it is thought to be comparatively much less abundant and less diverse than the human bacteriome. Additionally, most fungi are not easily cultured, even in specific media. Hence, their study has been limited to date, mainly because of the unavailability of methods used for their detection. However. the utilization of a novel metagenomic methodology will enable the identification of well-characterized mycobiomes in several parts of the human body and broaden our knowledge of their contribution to human health and disease. In this article, we review the role of the human mycobiome in the gut, respiratory organs, skin, genital tract, and carcinogenesis, highlighting the correlations between the human mycobiome and mycobiome-associated diseases. [ABSTRACT FROM AUTHOR]

The rhizospheric soil of medicinal plants plays a vital role in influencing secondary metabolites and overall plant health. These fungi influence the content of bioactive chemicals and essential oils while also promoting plant growth. They improve the medicinal value and plant resistance to biotic and abiotic stressors as bioinoculants. The purpose of this review is to investigate the diversity of rhizosphere fungi in medicinal plants, recognize important fungal groups and recurring patterns, and comprehend how these fungi contribute to the diversity of above-ground plant life. These realizations may result in sustainable and environmentally favorable methods of managing medicinal plant cultivation. [ABSTRACT FROM AUTHOR]

The preharvest maize mycobiome may be crucial in defining the health of the crop in terms of potential disease burden and mycotoxins. We investigated the preharvest maize mycobiome structure, including the influence of weather patterns, in terms of rainfall intensity, on its composition. In addition, we investigated correlation of genera Fusarium and Aspergillus with maize fumonisin-B1 and aflatoxin. Forty maize fields from selected districts in the wetter northern (N) and drier southern (S) agroecological zones of Zambia were sampled twice over two seasons (1 and 2). The defined weather variables over the two seasons were low rainfall with dry spell (S1), low rainfall (S2), and high rainfall (N1 and N2). High-throughput DNA amplicon sequencing of internal transcribed spacer 1 (ITS1) was used to determine the mycobiome structure and the composition in relation to rainfall patterns. We detected 61 genera, with Fusarium and previously unreported Sarocladium in Zambia to have the highest frequency of detection on the maize. There was a significant difference in fungal genera composition between S1 and S2 but no difference between N1 and N2. The weather pattern with dry spell, S1, had a strong proliferation of Meyerozyma and xerophiles Penicillium, Kodamaea, and Aspergillus. The four genera drove the difference in composition between S1 and S2 and the significantly higher fungal diversity in S1 compared to N2. Of the mycotoxin-important fungi, dry conditions (S1) were a key driver for proliferation of Aspergillus, while Fusarium proliferation occurred irrespective of weather patterns. The relative abundance of Aspergillus and Fusarium resonated with maize aflatoxin and fumonisin-B1 levels, respectively. IMPORTANCE Fungi contaminate various crops worldwide. Maize, an important human staple and livestock cereal, is susceptible to contamination with fungi in the field. Fungi are drivers of plant disease and can compromise yield. Some species of fungi are known to produce chemical compounds (mycotoxins), which are cancer-causing agents in humans and impair livestock productivity. It is important to understand the spectrum of fungi on maize and how weather conditions can impact their abundance. This is because the abundance of fungi in the field can have a bearing on the health of the crop as well as potential for mycotoxins contamination. By understanding the spectrum of the preharvest fungi, it becomes possible to know the key fungi adapted to the maize and subsequently the potential for crop disease as well as mycotoxins contamination. The influence of weather conditions on the spectrum of preharvest fungi on maize has not been fully explored. [ABSTRACT FROM AUTHOR]

The yeast Malassezia pachydermatis is a common inhabitant of the skin and mucosae of dogs. However, under certain circumstances this yeast can overgrow and act as an opportunistic pathogen causing otitis and dermatitis in dogs. Canine pododermatitis is a common disorder in dogs in which M. pachydermatis acts as an opportunistic pathogen. In the present study, the presence of Malassezia yeasts was assessed and quantified in samples collected from the interdigital space of dogs with pododermatitis before and after treatment, and from healthy dogs. The samples were subjected to two different cytological examinations, culture on Sabouraud glucose agar and modified Dixon's agar and a quantitative PCR targeting the internal transcribed spacer (ITS) genomic region. A selection of samples was analyzed by next generation sequencing (NGS) using the D1D2 domain of the large subunit of the ribosomal DNA as target. The pododermatitis samples before treatment showed higher cell counts, colony-forming units and ITS copies than the rest of samples. The NGS analysis revealed that Ascomycota was the main phylum in the healthy and post-treatment samples. However, Basidiomycota and M. pachydermatis was more abundant in the pododermatitis samples before treatment. These results support M. pachydermatis as an opportunistic agent in canine pododermatitis by a variety of methods, and demonstrate the correlation between cytologic and molecular methods for quantification. [ABSTRACT FROM AUTHOR]

The recent global pandemic of COVID-19 has predisposed a relatively high number of patients to acute respiratory distress syndrome (ARDS), which carries a risk of developing super-infections. Candida species are major constituents of the human mycobiome and the main cause of invasive fungal infections, with a high mortality rate. Invasive yeast infections (IYIs) are increasingly recognized as s complication of severe COVID-19. Despite the marked immune dysregulation in COVID-19, no prominent defects have been reported in immune cells that are critically required for immunity to Candida. This suggests that relevant clinical factors, including prolonged ICU stays, central venous catheters, and broad-spectrum antibiotic use, may be key factors causing COVID-19 patients to develop IYIs. Although data on the comparative performance of diagnostic tools are often lacking in COVID-19 patients, a combination of serological and molecular techniques may present a promising option for the identification of IYIs. Clinical awareness and screening are needed, as IYIs are difficult to diagnose, particularly in the setting of severe COVID-19. Echinocandins and azoles are the primary antifungal used to treat IYIs, yet the therapeutic failures exerted by multidrug-resistant Candida spp. such as C. auris and C. glabrata call for the development of new antifungal drugs with novel mechanisms of action.

Identifying microbial indicators of damp and moldy buildings remains a challenge at the intersection of microbiology, building science, and public health. Sixty homes in New York City were assessed for moisture-related damage, and three types of dust samples were collected for microbiological analysis. We applied four approaches for detecting fungal signatures of moisture damage in these buildings. Two novel targeted approaches selected specific taxa, identified by a priori hypotheses, from the broad mycobiome as detected with amplicon sequencing. We investigated whether (i) hydrophilic fungi (i.e., requiring high moisture) or (ii) fungi previously reported as indicating damp homes would be more abundant in water-damaged rooms/homes than in nondamaged rooms/homes. Two untargeted approaches compared water-damaged to non-water-damaged homes for (i) differences between indoor and outdoor fungal populations or (ii) differences in the presence or relative abundance of particular fungal taxa. Strong relationships with damage indicators were found for some targeted fungal groups in some sampling types, although not always in the hypothesized direction. For example, for vacuum samples, hydrophilic fungi had significantly higher relative abundance in water-damaged homes, but mesophilic fungi, unexpectedly, had significantly lower relative abundance in homes with visible mold. Untargeted approaches identified no microbial community metrics correlated with water damage variables but did identify specific taxa with at least weak positive links to water-damaged homes. These results, although showing a complex relationship between moisture damage and microbial communities, suggest that targeting particular fungi offers a potential route toward identifying a fungal signature of moisture damage in buildings.IMPORTANCE Living or working in damp or moldy buildings increases the risk of many adverse health effects, including asthma and other respiratory diseases. To date, however, the particular environmental exposure(s) from water-damaged buildings that causes the health effects have not been identified. Likewise, a consistent quantitative measurement that would indicate whether a building is water damaged or poses a health risk to occupants has not been found. In this work, we tried to develop analytical tools that would find a microbial signal of moisture damage amid the noisy background of microorganisms in buildings. The most successful approach taken here focused on particular groups of fungi-those considered likely to grow in damp indoor environments-and their associations with observed moisture damage. With further replication and refinement, this hypothesis-based strategy may be effective in finding still-elusive relationships between building damage and microbiomes.

Community assembly of crop-associated fungi is thought to be strongly influenced by deterministic selection exerted by the plant host, rather than stochastic processes. Here we use a simple, sorghum system with abundant sampling to show that stochastic forces (drift or stochastic dispersal) act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed, conditions when mycobiomes are small. Unexpectedly, we find no signal for stochasticity when drought stress is relieved, likely due to renewed selection by the host. In our experimental system, the host compartment exerts the strongest effects on mycobiome assembly, followed by the timing of plant development and lastly by plant genotype. Using a dissimilarity-overlap approach, we find a universality in the forces of community assembly of the mycobiomes of the different sorghum compartments and in functional guilds of fungi.

Abstract Multiple fungal species, including potential opportunistic pathogens have been previously identified in water systems. Here, we investigated over 250 restroom sink fungal communities across a university campus and evaluated their diversity and core taxa present. Remarkable similarity in mycobial community composition was observed across buildings with Ascomycota consistently dominating. We found a core mycobiome independent of the building sampled, that included Exophiala species, potential opportunistic pathogenic black yeasts. Other prevalent and dominant taxa included Saccharomyces and Fusarium, common built environment fungi. The frequent presence of Malassezia, a common skin commensal, showed the external influence of human activities as a source of fungi to sinks. The study represents a novel exploration of sink P‐traps mycobial communities from a public area and highlights their importance as reservoirs of possible pathogenic fungi, as well as emphasizing the relevance of further research in this understudied ecosystem within the built environment.

Jinkun Xia,1,2,* Haoran Ding,1,* Shujun Liu,3 Ran An,1,2 Xiaolei Shi,1– 3 Ming Chen,1 Haozhen Ren1– 3 1Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, People’s Republic of China; 2Institute of Hepatobiliary Surgery, Medical School, Nanjing University, Nanjing, People’s Republic of China; 3Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Haozhen Ren; Ming Chen, Email renhaozhen1984@163.com; chenming@njglyy.comAbstract: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors of the digestive system worldwide, and there is a lack of effective treatment for late-stage HCC. Recent experimental studies have demonstrated that dysfunction of the intestinal flora has a significant impact on hepatocarcinogenesis. The pathophysiological link between the intestine, its microbiota, and the liver has been described as the “gut-liver axis”. Dysbiosis of the intestinal flora and increased permeability of the intestinal wall are closely associated with liver pathology through the immune response. The “gut-liver axis” theory has been applied to the clinical study of the pathogenesis and treatment of HCC. The intestinal fungal community, as part of the gut microbiome, has a significant impact on human health and disease, while relatively little research has been done in HCC. In this study, we performed a comprehensive analysis of the expression and potential biological functions of the fungal recognition receptors C-type lectin receptors (CLRs) (Dectin-1, Dectin-2, Dectin-3, and Mincle) in HCC. We found that CLRs were downregulated in HCC, and their expressions were correlated with the clinical prognosis of HCC patients. Further studies suggested that the expression of CLRs were significantly correlated with immune infiltration and immunotherapy efficacy in HCC. Based on previous studies and our findings, we hypothesize that intestinal fungal communities and CLRs-triggered antifungal immunity have a key role in the pathogenesis of HCC, and these findings may provide new perspectives and targets for HCC immunotherapy.Keywords: hepatocellular carcinoma, mycobiome, fungus, immunity, C-type lectin receptor, gut-liver axis

BackgroundHispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment.ResultsAmplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA.ConclusionsOur analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the “mycobiome” of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate (“sputum”) samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.

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 To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.

Metabarcoding is an effective and cost-efficient approach to study environmental microbiomes and has become a standard method in studying microbial community structures and relative species abundance. In grapevine research on leaf microbial communities, two kinds of sample types, either leaf wash sediments representing the phyllosphere microbiome from leaf surfaces or leaf tissue samples, e.g., leaf disks, including phyllosphere and endosphere microorganisms, are used to characterize leaf microbiomes. The goal of this study was to analyze the advantages and disadvantages of these sample preparation methods for the characterization of the phyllosphere microbiome by fungal metabarcoding with both sample types being processed from the exact same set of leaves. We used a metabarcoding strategy, which can detect Fungi and Oomycetes, facilitating the parallel analysis of these communities. At each sampling time point, species richness was shown to be higher in leaf wash samples, and differences in the community structure between samples was smaller for this sample type as well. Furthermore, by comparing read count abundance to qPCR measured relative proportions of selected amplicon sequence variants, a higher congruence was observed for leaf wash samples. Therefore, metabarcoding analyses of leaf samples using leaf wash sediments outperform analyses using leaf disks and should be applied to characterize phyllosphere fungal communities. As a second goal, we show that the direct comparison of metabarcoding libraries of both sample types prepared from the exact same set of leaves also provides a new strategy to identify endophytes that may not be culturable. [Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Background: Until recently, the properties of microbiome and mycobiome in humans and its relevance to disease have largely been unexplored. While the interest of microbiome and malignancy over the past few years have burgeoned with advent of new technologies, no research describing the composition of mycobiome in bladder cancer has been done. Deciphering of the metagenome and its aggregate genetic information can be used to understand the functional properties and relationships between the bacteria, fungi, and cancer. Objective: The aim of this project is to characterize the compositional range of the normal versus bladder cancer mycobiome of the gut. Design, setting, and participants: An internal transcribed spacer (ITS) survey of 52 fecal samples was performed to evaluate the gut mycobiome differences between noncancer controls and bladder cancer patients. Outcome measurements and statistical analysis: Our study evaluated the differences in mycobiome among patients with bladder cancer, versus matched controls. Our secondary analysis evaluated compositional differences in the gut as a function of response status with neoadjuvant chemotherapy. Data demultiplexing and classification were performed using the QIIME v.1.1.1.1 platform. The Ion Torrent–generated fungal ITS sequence data were processed using QIIME (v.1.9.1), and the reads were demultiplexed, quality filtered, and clustered into operation taxonomic units using default parameters. Alpha and beta diversity were computed and plotted in Phyloseq, principal coordinate analysis was performed on Bray-Curtis dissimilarity indices, and a one-way permutational multivariate analysis of variance was used to test for significant differences between cohorts. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition. Results and limitations: We found distinctive mycobiome differences between control group (n = 32) and bladder cancer (n = 29) gut flora, and identified an increasing abundance of Tremellales, Hypocreales, and Dothideales. Significant differences in alpha and beta diversity were present between the groups (control vs bladder; p = 0.002), noting distinct compositions within each cohort. A subgroup analysis by sex and neoadjuvant chemotherapy status did not show any further differences in mycobiome composition and diversity. Our results indicate that the gut mycobiome may modulate tumor response to preoperative chemotherapy in bladder cancer patients. We propose that patients with a “favorable” mycobiome composition (eg, high diversity, and low abundance of Agaricomycetes and Saccharomycetes) may have enhanced systemic immune response to chemotherapy through antigen presentation. Conclusions: Our study is the first to characterize the enteric mycobiome in patients with bladder cancer and describe complex ecological network alterations, indicating complex bacteria-fungi interactions, particularly highlighted among patients with complete neoadjuvant chemotherapy response. Patient summary: Our study has demonstrated that the composition of stool mycobiome (fungal inhabitants of the gastrointestinal tract) in patients with bladder cancer is different from that in noncancer individuals. Furthermore, when evaluating how patients respond to chemotherapy given prior to their surgery, our study noted significant differences between patients who responded and those who did not.

An altered gut microbiota is a possible contributing pathogenic factor in myasthenia gravis (MG), an autoimmune neuromuscular disease. However, the significance of the fungal microbiome is an understudied and neglected part of the intestinal microbiome in MG. We performed a sub-analysis of the MYBIOM study including faecal samples from patients with MG (n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers (n = 12) by sequencing the internal transcribed spacer 2 (ITS2). Fungal reads were obtained in 51 out of 77 samples. No differences were found in alpha-diversity indices computed between the MG, NIND, CIDP and HV groups, indicating an unaltered fungal diversity and structure. Overall, four mould species (Penicillium aurantiogriseum, Mycosphaerella tassiana, Cladosporium ramonetellum and Alternaria betae-kenyensis) and five yeast species (Candida. albicans, Candida. sake, Candida. dubliniensis, Pichia deserticola and Kregervanrija delftensis) were identified. Besides one MG patient with abundant Ca. albicans, no prominent dysbiosis in the MG group of the mycobiome was found. Not all fungal sequences within all groups were successfully assigned, so further sub-analysis was withdrawn, limiting robust conclusions. [ABSTRACT FROM AUTHOR]

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]

Background: Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with "shotgun" metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis. Results: Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets, mock community standards, and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel strains. Finally, we deploy CORRAL on our MicrobiomeDB.org resource, producing an atlas of eukaryotes present in various environments of the human body and linking their presence to study covariates. Conclusions: CORRAL allows eukaryotic detection to be automated and carried out at scale. Implementation of CORRAL in MicrobiomeDB.org creates a running atlas of microbial eukaryotes in metagenomic studies. Since our approach is independent of the reference used, it may be applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as the identification of bacterial virulence genes or taxonomic classification of viral reads. 7wGjTT9at-YHUAvLa_r2RM Video Abstract [ABSTRACT FROM AUTHOR]

Background: Increasing data indicates the gut flora including bacteria and fungi combined with environmental factors are important in the pathogenesis of colorectal cancer (CRC). Understanding differences in the microbiome in patients with colon neoplasia will foster the development of biomarkers for early detection. Aims: Determine the association of microbiome with presence of adenomas and predicted CRC risk. Methods: In subjects referred for colonoscopy, the NCI CRC risk assessment tool was completed and stool for microbiome analysis as well as fecal immunochemical test (FIT) were collected. We calculated the microbiome alpha diversity using the Shannon index as well as individual bacterial and fungal species. Results: Among 34 patients, we identified 10 with one or more adenomas. Only 2 patients were FIT positive. The median predicted lifetime CRC risk was 2.75% and the prevalence of adenoma was higher in the fourth quartile (P < 0.001). The measured alpha diversity was somewhat higher in patients with adenomas (P = 0.07). We identified 4 bacterial species with an increased relative abundance among patients with adenomas [P < 0.5]. Lifetime CRC risk was associated with 2 specific bacterial species, P. distasonis & E. hermannii [P = 0.05 & 0.09, respectively]. No associations were seen with fungal species and adenoma prevalence or lifetime CRC risk. Conclusions: In addition to a strong correlation of predicted CRC risk and adenoma prevalence, we also found important differences in specific bacterial species and both adenoma prevalence and CRC risk. Larger trials are needed to potentially implement further data in the clinical setting. [ABSTRACT FROM AUTHOR]

The black morel Morchella sextelata (Morchellaceae, Pezizales) is a valuable edible mushroom that can be cultivated on a large scale, but a severe yield decline is observed during continuous cropping. The effect of long-term cropping on soil-borne diseases and the dysbiosis of the microbiome and how these biotic factors affect the morel yield are not well understood. To help fill this knowledge gap, we designed an indoor experiment to investigate the influence of black morel cropping regimes on soil physicochemical properties, richness and distribution of fungal community, and morel primordial production. In this study, we employed rDNA metabarcoding and microbial network analysis to evaluate the effect of non-continuous and continuous cropping regimes on the fungal community during three developmental stages of black morel production, namely, the bare soil mycelium, mushroom conidial, and primordial stages. The results showed that during the first year, M. sextelata mycelium overwhelmed the resident soil fungal community by reducing the alpha diversity and niche breadth of soil fungal patterns by a greater amount compared to the continuous cropping regime, leading to high crop yield of 12.39 ± 6.09/quadrat but less complex soil mycobiome. To sustain continuous cropping, exogenous nutrition bags and morel mycelial spawn were consecutively added to the soil. The additional nutrient input stimulated the growth of fungal saprotrophic decomposers. The degrading activity of soil saprotrophs, including M.sextelata, caused a significant increase in soil nutrient content. This led to an inhibitory effect on the formation of morel primordia, resulting in a sharp decline to 0.29 ± 0.25/quadrat and 0.17 ± 0.24/quadrat, respectively, in the final morel cropping. Our findings provided a dynamic overview of the soil fungal community during morel mushroom production, allowing us to identify beneficial and detrimental fungal taxa in the soil mycobiome involved in morel cultivation. The information acquired from this study can be applied to mitigate the adverse impact of continuous cropping on the yield of black morel. [ABSTRACT FROM AUTHOR]

The microbiome consists mostly of bacteria, but new evidence and developments in sequencing methods have shown that fungi play an important role in human health and in the stability of the microbiota. Scientific knowledge about the role of commensal fungi in intestinal, oral, vaginal and cutaneous communities has been increasing; however, more studies are still needed to better understand their action in these niches. To date, fungal research focuses primarily on opportunistic diseases caused by fungal species, leaving unclear the possible role of fungi as an integral part of the microbiota. Although they are much less abundant than bacteria, fungi such as species belonging to the genus Candida, Malassezia, Rhodotorula and Cryptococcus are some of the yeasts that have been in the focus of the scientific community because they inhabit various niches. In this review, we have summarized the current information about the yeasts that inhabit the human body, including some of the diseases that they can cause when the microbiota becomes unstable. [ABSTRACT FROM AUTHOR]

The symbiotic relationship between macroorganisms, such as plants and animals, and the microorganisms in their environment plays a crucial role in shaping their physiology and ecology. Thus, many studies have examined microbial symbiosis in relation to plants, humans, and insects. However, little is known about the microbial diversity associated with isopods. Hence, in this study, we investigated the fungal diversity associated with two species of terrestrial isopods, Armadillidium nasatum and A. vulgare. In this study, we used a metabarcoding approach to compare fungal diversity between the two species for the first time. Our results indicated that A. nasatum had significantly greater mycobiome alpha diversity than A. vulgare. In contrast, fungal communities (beta diversity) did not differ significantly between hosts, except in beta dispersion of relative abundance. The majority of fungi identified belonged to Ascomycota and Basidiomycota, phyla that are dominated by saprotrophs. In conclusion, our findings shed light on the fungal communities associated with Armadillidium species, providing valuable insight into the biology of terrestrial isopods. [ABSTRACT FROM AUTHOR]

Rationale: Emerging data support the existence of a microbial “gut-lung” axis that remains unexplored in bronchiectasis. Methods: Prospective and concurrent sampling of gut (stool) and lung (sputum) was performed in a cohort of n = 57 individuals with bronchiectasis and subjected to bacteriome (16S rRNA) and mycobiome (18S Internal Transcribed Spacer) sequencing (total, 228 microbiomes). Shotgun metagenomics was performed in a subset (n = 15; 30 microbiomes). Data from gut and lung compartments were integrated by weighted similarity network fusion, clustered, and subjected to co-occurrence analysis to evaluate gut-lung networks. Murine experiments were undertaken to validate specific Pseudomonas-driven gut-lung interactions. Results: Microbial communities in stable bronchiectasis demonstrate a significant gut-lung interaction. Multibiome integration followed by unsupervised clustering reveals two patient clusters, differing by gut-lung interactions and with contrasting clinical phenotypes. A high gut-lung interaction cluster, characterized by lung Pseudomonas, gut Bacteroides, and gut Saccharomyces, is associated with increased exacerbations and greater radiological and overall bronchiectasis severity, whereas the low gut-lung interaction cluster demonstrates an overrepresentation of lung commensals, including Prevotella, Fusobacterium, and Porphyromonas with gut Candida. The lung Pseudomonas-gut Bacteroides relationship, observed in the high gut-lung interaction bronchiectasis cluster, was validated in a murine model of lung Pseudomonas aeruginosa infection. This interaction was abrogated after antibiotic (imipenem) pretreatment in mice confirming the relevance and therapeutic potential of targeting the gut microbiome to influence the gut-lung axis. Metagenomics in a subset of individuals with bronchiectasis corroborated our findings from targeted analyses. Conclusions: A dysregulated gut-lung axis, driven by lung Pseudomonas, associates with poorer clinical outcomes in bronchiectasis. [ABSTRACT FROM AUTHOR]

Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype - two factors that are likely to differ between farms - on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core 'candidates', which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production. [ABSTRACT FROM AUTHOR]

As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi. [ABSTRACT FROM AUTHOR]

Background: The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region. Results: Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars. Conclusions: Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors. [ABSTRACT FROM AUTHOR]

The MycoPins method described here is a rapid and affordable protocol to monitor early colonization events in communities of wood-inhabiting fungi in fine woody debris. It includes easy to implement field sampling techniques and sample processing, followed by data processing, and analysis of the development of early dead wood fungal communities. The method is based on fieldwork from a time series experiment on standard sterilized colonization targets followed by the metabarcoding analysis and automated molecular identification of species. This new monitoring method through its simplicity, moderate costs, and scalability paves a way for a broader and scalable project pipeline. MycoPins establishes a standard routine for research stations or regularly visited field sites for monitoring of fungal colonization of woody substrates. The routine uses widely available consumables and therefore presents a unifying method for monitoring of fungi of this type. [ABSTRACT FROM AUTHOR]

Background: Suboptimal maternal oral health during pregnancy is potentially associated with adverse birth outcomes and increased dental caries risks in children. This study aimed to assess the oral microbiome and immune response following an innovative clinical regimen, Prenatal Total Oral Rehabilitation (PTOR), that fully restores women's oral health to a "disease-free status" before delivery. Methods: This prospective cohort study assessed 15 pregnant women at baseline and 3 follow-up visits (1 week, 2 weeks, and 2 months) after receiving PTOR. The salivary and supragingival plaque microbiomes were analyzed using metagenomic sequencing. Multiplexed Luminex cytokine assays were performed to examine immune response following PTOR. The association between salivary immune markers and oral microbiome was further examined. Results: PTOR was associated with a reduction of periodontal pathogens in plaque, for instance, a lower relative abundance of Tannerella forsythia and Treponema denticola at 2 weeks compared to the baseline (p < 0.05). The alpha diversity of plaque microbial community was significantly reduced at the 1-week follow-up (p < 0.05). Furthermore, we observed significant changes in the Actinomyces defective-associated carbohydrate degradation pathway and Streptococcus Gordonii-associated fatty acid biosynthesis pathway. Two immune markers related to adverse birth outcomes significantly differed between baseline and follow-up. ITAC, negatively correlated with preeclampsia severity, significantly increased at 1-week follow-up; MCP-1, positively correlated with gestational age, was elevated at 1-week follow-up. Association modeling between immune markers and microbiome further revealed specific oral microorganisms that are potentially correlated with the host immune response. Conclusions: PTOR is associated with alteration of the oral microbiome and immune response among a cohort of underserved US pregnant women. Future randomized clinical trials are warranted to comprehensively assess the impact of PTOR on maternal oral flora, birth outcomes, and their offspring's oral health. [ABSTRACT FROM AUTHOR]

Although the human bacteriome and virome have gained a great deal of attention over the years, the human mycobiome has been far more neglected despite having significant value and implications in human health. In women, mycobiome profiles in breastmilk, vaginal regions, the gut, skin, and the oral cavity can provide insight into women's health, diseases, and microbiome dysbiosis. Analyses of mycobiome composition under factors, such as health, age, diet, weight, and drug exposure (including antibiotic therapies), help to elucidate the various roles of women's mycobiome in homeostasis, microbiome interactions (synergistic and antagonistic), and health. This review summarizes the most recent updates to mycobiome knowledge in these critical areas. [ABSTRACT FROM AUTHOR]

This manuscript presents the results of an exploratory study on the relationships between NF-kB response through Toll-like receptor (TLR) activation by dust characterized by fungal spore concentrations and species diversity. Personal total dust samples were collected from Norwegian waste sorting plants and then characterized for fungal spores and fungal species diversity, as well as for other bioaerosol components, including endotoxins and actinobacteria. The ability of the dust to induce an NF-kB response by activating TLR2 and TLR4 in vitro was evaluated, as well as the relationship between such responses and quantifiable bioaerosol components. The average concentrations of bioaerosols were 7.23 mg total dust m-3, 4.49 x 105 fungal spores m-3, 814 endotoxin units m-3, and 0.6 x 105 actinobacteria m-3 . The mean diversity measurements were 326, 0.59, and 3.39 for fungal richness, evenness, and Shannon index, respectively. Overall, fungal operational taxonomic units (OTUs) belonging to the Ascomycota phylum were most abundant (55%), followed by Basidiomycota (33%) and Mucoromycota (3%). All samples induced significant NF-kB responses through TLR2 and TLR4 activation. While fungal spore levels were positively associated with TLR2 and TLR4 activation, there was a trend that fungal species richness was negatively associated with the activation of these receptors. This observation supports the existence of divergent immunological response relationships between TLR activation and fungal spore levels on one hand and between TLR activation and fungal species diversity on the other. Such relationships seem to be described for the first time for dust from waste facilities. IMPORTANCE This manuscript presents results on multifactorial characterization of bioaerosol exposure in Norwegian waste sorting plants and the potential of such airborne dust to induce NF-kB reactions through TLR2 and TLR4 activations in an in vitro reporter cell model system. Our data revealed that increasing fungal spore levels in the dust is associated with increased activation of TLR2 and TLR4, whereas increasing fungal OTU richness is associated with decreasing activation of these receptors. The NF-kB-induced responses by the collected dust represent, therefore, effective measures of potential key immunological effects induced by a complex mixture of hazardous components, including characterized factors such as endotoxins, fungal spores, bacteria, and many other uncharacterized components. The key immunological events reported here are suggested as holistic alternatives to today’s bioaerosol exposure characterization approaches for epidemiological studies in the future. [ABSTRACT FROM AUTHOR]