The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing applications, the structure and composition of mycobiome in the mouth, lung, gut, vagina, and skin have been analyzed, and the role of microbiome in diseases has been investigated. Mycobiome also influences the composition of bacteriome and includes key species that maintain the structure and function of microbial communities. Fungi also influence host immune responses. In this review, we summarized the mycobiome com-position at various sites and different diseases and the interactions between fungi-bacteria and fungi-host.
Bacteria ; Disease ; Female ; Fungi ; Humans ; Microbiota ; Mouth ; Mycobiome

This study is aimed to reveal the rhizosphere soil fungal community structure difference of Coptis chinensis cropping between natural forest and artificial shed modes, and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under natural forest and artificial shed modes were collected. Illumina high-throughput sequencing technology was used to analyze the community structure and diversity of soil fungi under the tow cropping modes,and the effects of soil nutriment indices on soil fungal community structure. The results suggested that the abundance and diversity of fungal communities in soil of 2-5-year-old C. chinensis were not significant different in both two cropping modes, but it was significantly higher than that in the 1-year-old C. chinensis. Comparing soil samples from the same year-old C. chinensis under the two cropping modes, it was found that there was no significant difference in the abundance and diversity of fungal communities. The fungal community of the rhizosphere soil was different in composition and abundance between tow cropping modes, and between different planting years. The 17 phyla,59 classes and 155 orders,and 17 phyla,59 classes and 157 orders were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest and the artificial shed, respectively. Ascomycota, Basidiomycota and Mortierellomycota were dominant phyla in rhizosphere soil, and the average abundance of the 3 phyla accounted for 74.36% and 74.30% of the total fungi. The results of analysis of similarities showed that there were significant differences in the fungal community structure of 1-year-old and 2-year-old C. chinensis soil fungi, and there was no significant difference in the community structure of 3-5-year-old samples. Under the natural forest cropping mode, there were significant differences among the samples of different years. Under the artificial shed cropping, there were significant differences in fungal community structure between 1-year-old and 3-5-year-old C. chinensis soil, and between 2-year-old and 3-5-year-old C. chinensis soil. The results of canonical correlation analysis showed that soil pH and soil organic matter content were the main factors affecting the soil fungal community structure. Soil organic matter content was positively correlated with Basidiomycota and Cryptomycota, pH was negatively correlated with Basidiomycota and C. ryptomycota. The planting of C. chinensis has promoted the diversity and abundance of rhizosphere fungal community significantly. For the same year-old C. chinensis soil, abundance of fungal community was no significant difference between two cropping modes. There are significant differences in the rhizosphere soil fungal community structure between tow cropping modes in the first two years of planting. Through the interaction between the rhizosphere and the soil and the continuous selection of the rhizosphere to the fungal community, the fungal community structure tended to be the same between the two cropping modes in rhizosphere soil of 3-5-year old C. chinensis. The soil pH and orga-nic matter content were the main factors affecting the change of fungal community structure.
Coptis ; Forests ; Fungi ; Mycobiome ; Plant Roots ; Rhizosphere ; Soil ; Soil Microbiology

In the process of harvesting, production and processing, storage, and transportation, the traditional Chinese medicine Platycladi Semen is prone to mildew due to its own and environmental factors, which can nourish the production of toxic or pathogenic fungi, and even produce mycotoxins, which affects the safety of clinical medication. The 2020 edition of Chinese Pharmacopoeia limits the highest standard of aflatoxin content in Platycladi Semen. However, there are few studies on the fungal contamination of Platycladi Semen, and it is difficult to prevent and control it in a targeted manner. Therefore, based on the Illumina NovaSeq6000 platform, this article uses ITS sequence amplicon technology to analyze the distribution and diversity of fungi in 27 batches of commercially available Platycladi Semen in the Chinese market. A total of 10 phyla, 35 classes, 93 orders, 193 families, 336 genera, and 372 species of fungi were identified in China. Among them, Aspergillus, Alternaria spp. were dominant, 20 batches of samples were detected for A. flavus, 10 batches of samples were detected for A. nidulans, and all samples were detected for potential pathogenic fungi such as A. fumigatus and A. niger. According to diversity analysis, the diversity of the fungal communities in the samples from Gansu province was high, the samples in Shandong province contain the largest number of fungal species, and the samples in Guangxi province had the lo-west diversity and the least number of species. In most samples, pathogenic fungi such as A. fumigatus, A. niger, A. flavus, A. parasiticus were detected in varying degrees. This study systematically investigated the fungal contamination of Platycladi Semen from the markets in the last link of the its industrial chain, and clarified the distribution of Platycladi Semen fungi, especially toxin-producing fungi, and provided theoretical basis for the targeted prevention and control of fungal contamination in Platycladi Semen.
Aflatoxins ; China ; Fungi/genetics* ; Humans ; Mycobiome ; Mycotoxins/analysis* ; Semen/chemistry*

The continuous cropping obstacle of Gastrodia elata is outstanding, but its mechanism is still unclear. In this study, microbial changes in soils after G. elata planting were investigated to explore the mechanism correlated with continuous cropping obstacle. The changes of species and abundance of fungi and bacteria in soils planted with G. elata after 1, 2, and 3 years were compared. The pathogenic fungi that might cause continuous cropping diseases of G. elata were isolated. Finally, the prevention and control measures of soil-borne fungal diseases of G. elata were investigated with the rotation planting pattern of "G. elata-Phallus impudicus". The results showed that G. elata planting resulted in the decrease in bacterial and fungal community stability and the increase in harmful fungus species and abundance in soils. This change was most obvious in the second year after G. elata planting, and the soil microbial community structure could not return to the normal level even if it was left idle for another two years. After G. elata planting in soils, the most significant change was observed in Ilyonectria cyclaminicola. The richness of the Ilyonectria fungus in soils was significantly positively correlated with the incidence of G. elata diseases. When I. cyclaminicola was inoculated in the sterile soil, the rot rate of G. elata was also significantly increased. After planting one crop of G. elata and one to three crops of P. impudicus, the fungus community structure in soils gradually recovered, and the abundance of I. cyclaminicola decreased year by year. Furthermore, the disease rate of G. elata decreased. The results showed that the cultivation of G. elata made the Ilyonectria fungi the dominant flora in soils, and I. cyclaminicola served as the main pathogen of continuous cropping diseases of G. elata, which could be reduced by rotation planting with P. impudicus.
Bacteria ; Fungi ; Gastrodia/microbiology* ; Mycobiome ; Soil ; Soil Microbiology

This study aimed to analyze aflatoxins content and fungal community distribution in the harvesting and processing of Platycladi Semen, and explore the key link that affects aflatoxins contamination. The related Platycladi Semen samples of different maturity periods(cone non-rupture period, early rupture, and complete rupture period) and different processing periods(before drying, during 2-d drying, during 7-d drying, before and after seed scale removal, before and after peeling, 1 d after color sorting, and 7 d after color sorting) were collected for identifying the fungal community composition on sample surface by ITS amplicon sequencing. Then the content of aflatoxins B_1, B_2, G_1 and G_2 was determined by HPLC-MS/MS. The results showed that during the harvesting of Platycladi Semen from cone non-rupture to complete rupture, aflatoxins were only detected in the seed scale and seed coat, with aflatoxin G_2 in the seed scale and aflatoxin B_1 in the seed coat. During the drying, with the prolongation of drying time, aflatoxins B_1 and G_2 were detected simultaneously in the seed scale, aflatoxin B_1 in the seed coat, and low-content aflatoxin B_1 in the seed kernel. During subsequent processing, the aflatoxin content in seed kernel during subsequent processing was slighted increased. As demonstrated by fungal detection, Aspergillus flavus was not present during the harvesting of Platycladi Semen, but present during the drying and processing. Its content in the seed coat during the drying process was relatively higher. In short, Platycladi Semen should be harvested as soon as possible after it becomes fully mature. Drying process is the key link of preventing aflatoxin contamination. It is advised to build a sunlight room or adopt similar settings, standardize the operations in other processes, and keep the surrounding environment clean to minimize aflatoxin contamination.
Aflatoxins/analysis* ; Aspergillus flavus ; Food Contamination/prevention & control* ; Mycobiome ; Semen/chemistry* ; Tandem Mass Spectrometry

The biodiversity of the mycobiome, an important component of the oral microbial community, and the roles of fungal-bacterial and fungal-immune system interactions in the pathogenesis of oral lichen planus (OLP) remain largely uncharacterized. In this study, we sequenced the salivary mycobiome and bacteriome associated with OLP. First, we described the dysbiosis of the microbiome in OLP patients, which exhibits lower levels of fungi and higher levels of bacteria. Significantly higher abundances of the fungi Candida and Aspergillus in patients with reticular OLP and of Alternaria and Sclerotiniaceae_unidentified in patients with erosive OLP were observed compared to the healthy controls. Aspergillus was identified as an "OLP-associated" fungus because of its detection at a higher frequency than in the healthy controls. Second, the co-occurrence patterns of the salivary mycobiome-bacteriome demonstrated negative associations between specific fungal and bacterial taxa identified in the healthy controls, which diminished in the reticular OLP group and even became positive in the erosive OLP group. Moreover, the oral cavities of OLP patients were colonized by dysbiotic oral flora with lower ecological network complexity and decreased fungal-Firmicutes and increased fungal-Bacteroidetes sub-networks. Third, several keystone fungal genera (Bovista, Erysiphe, Psathyrella, etc.) demonstrated significant correlations with clinical scores and IL-17 levels. Thus, we established that fungal dysbiosis is associated with the aggravation of OLP. Fungal dysbiosis could alter the salivary bacteriome or may reflect a direct effect of host immunity, which participates in OLP pathogenesis.
Adult ; Bacteria ; isolation & purification ; Case-Control Studies ; Dysbiosis ; complications ; microbiology ; Female ; Humans ; Lichen Planus, Oral ; complications ; microbiology ; Male ; Microbiota ; Middle Aged ; Mouth Mucosa ; microbiology ; Mycobiome ; Saliva ; microbiology