Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis

Evaluation of Cordyceps sinensis Quality in 15 Production Areas Using Metabolomics and the Membership Function Method

Cordyceps sinensis is a precious medicinal and edible fungus, which is widely used in body health care and disease prevention. The current research focuses on the comparison of metabolite characteristics between a small number of samples and lacks a comprehensive evaluation of the quality of C. sinensis in a large-scale space. In this study, LC-MS/MS, principal component analysis (PCA), hierarchical cluster analysis (HCA), and the membership function method were used to comprehensively evaluate the characteristics and quality of metabolites in 15 main producing areas of C. sinensis in China. The results showed that a total of 130 categories, 14 supercategories, and 1718 metabolites were identified. Carboxylic acids and derivatives, fatty acyls, organo-oxygen compounds, benzene and substituted derivatives, prenol lipids, and glycerophospholipids were the main components of C. sinensis. The HCA analysis and KEGG pathway enrichment analysis of 559 differentially accumulated metabolites (DAMs) showed that the accumulation models of fatty acids and conjugates and carbohydrates and carbohydrate conjugates in glycerophospholipid metabolism and arginine and proline metabolism may be one of the reasons for the quality differences in C. sinensis in different producing areas. In addition, a total of 18 biomarkers were identified and validated, which had a significant discrimination effect on the samples (p < 0.05). Overall, YS, BR, and ZD, with the highest membership function values, are rich and balanced in nutrients. They are excellent raw materials for the development of functional foods and provide scientific guidance for consumers to nourish health care.

UvHOS3-mediated histone deacetylation is essential for virulence and negatively regulates ustilaginoidin biosynthesis in Ustilaginoidea virens

Ustilaginoidea virens is the causal agent of rice false smut, which has recently become one of the most important rice diseases worldwide. Ustilaginoidins, a major type of mycotoxins produced in false smut balls, greatly deteriorates grain quality. Histone acetylation and deacetylation are involved in regulating secondary metabolism in fungi. However, little is yet known on the functions of histone deacetylases (HDACs) in virulence and mycotoxin biosynthesis in U. virens. Here, we characterized the functions of the HDAC UvHOS3 in U. virens. The ΔUvhos3 deletion mutant exhibited the phenotypes of retarded growth, increased mycelial branches and reduced conidiation and virulence. The ΔUvhos3 mutants were more sensitive to sorbitol, sodium dodecyl sulphate and oxidative stress/H2 O2 . ΔUvhos3 generated significantly more ustilaginoidins. RNA-Seq and metabolomics analyses also revealed that UvHOS3 is a key negative player in regulating secondary metabolism, especially mycotoxin biosynthesis. Notably, UvHOS3 mediates deacetylation of H3 and H4 at H3K9, H3K18, H3K27 and H4K8 residues. Chromatin immunoprecipitation assays indicated that UvHOS3 regulates mycotoxin biosynthesis, particularly for ustilaginoidin and sorbicillinoid production, by modulating the acetylation level of H3K18. Collectively, this study deepens the understanding of molecular mechanisms of the HDAC UvHOS3 in regulating virulence and mycotoxin biosynthesis in phytopathogenic fungi.

Exploring the roles of microorganisms and metabolites in the 30-year aging process of the dried pericarps of Citrus reticulata 'Chachi' based on high-throughput sequencing and comparative metabolomics

GuangChenpi (GCP), the dried pericarps of Citrus reticulata 'Chachi', has been consumed daily as a food and dietary supplement in China for centuries. Its health benefits are generally recognized to be dependent on storage time. However, the specific roles of microorganisms and metabolites during long-term storage are still unclear. In this study, comparative metabolomics and high-throughput sequencing techniques were used to investigate the effects of co-existing microorganisms on the metabolites in GCP stored from 1 to 30 years. In total, 386 metabolites were identified and characterized. Most compounds were flavonoids (37%), followed by phenolic acids (20%). Seventeen differentially upregulated metabolites were identified as potential key metabolites in GCP, and 8 of them were screened out as key active ingredients by Venn diagram comparative analyses and verified by network pharmacology and molecular docking. In addition, long-term storage could promote the accumulation of secondary metabolites. Regarding the GCP microbiota, Xeromyces dominated the whole 30-year aging process.Moreover, Spearman correlation analysis indicated that Bacillus thuringiensis and Xeromyces bisporus, the dominant bacterial and fungal species, were strongly associated with the key active metabolites. Our results suggested that the change of active ingredients caused by the dominant microbial is one of the mechanisms affecting the GCP aging process. Our study provides novel functional insights and research perspectives on microorganism-associated metabolite changes that may improve the GCP aging process.

Transcriptome and Metabolome Analyses of Thitarodes xiaojinensis in Response to Ophiocordyceps sinensis Infection

Ophiocordyceps sinensis exhibits more than 5 months of vegetative growth in Thitarodes xiaojinensis hemocoel. The peculiar development process of O. sinensis has been elucidated through morphological observation and omics technology; however, little information has been reported regarding the changes that occur in the host T. xiaojinensis. The RNA sequencing data showed that when O. sinensis blastospores were in the proliferative stage, the greatest change in the infected larval fat body was the selectively upregulated immune recognition and antimicrobial peptide genes. When O. sinensis blastospores were in the stationary stage, the immune pathways of T. xiaojinensis reverted to normal levels, which coincides with the successful settlement of O. sinensis. Pathway enrichment analysis showed a higher expression of genes involved in energy metabolism pathway in this stage. Metabolomic analyses revealed a reduction of amino acids and lipids in hemolymph, but an upregulation of lipids in the fat body of the host larvae after O. sinensis infection. We present the first transcriptome integrated with the metabolome study of T. xiaojinensis infected by O. sinensis. It will improve our understanding of the interaction mechanisms between the host and entomopathogenic fungi, and facilitate future functional studies of genes and pathways involved in these interactions.

Fractional extraction and structural characterization of glycogen particles from the whole cultivated caterpillar fungus Ophiocordyceps sinensis

Ophiocordyceps sinensis (syn. Cordyceps sinensis) is a valuable medicinal fungus in traditional Chinese medicine, and one or more polysaccharides are the key constituents with important medical effects. Glycogen as a functional polysaccharide is widely identified in eukaryotes including fungi. However, there is no definitive report of glycogen presence in O. sinensis. In this study, we carefully fractionated polysaccharides from cultivated caterpillar fungus O. sinensis, which were then characterized via methods for glycogen analysis. According to the results, 1.03 ± 0.43 % of polysaccharides were quantified via amyloglucosidase digestion in the whole cultivated caterpillar fungus, which had a typical spherical shape under transmission electron microscope with an average peak radius of 37.63 ± 0.57 nm via size exclusion chromatography and an average chain length of 12.47 ± 0.94 degree of polymerization via fluorophore-assisted capillary electrophoresis. Taken together, this study confirmed that the polysaccharides extracted form O. sinensis were mostly glycogen.

Integrated metabolomics and transcriptomics reveal metabolites difference between wild and cultivated Ophiocordyceps sinensis

Ophiocordyceps sinensis is a traditional medicinal fungus endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. The scarcity of the wild resource has led to increased attention to artificially cultivated O. sinensis. However, little is known about the metabolic differences and the regulatory mechanisms between cultivated and wild O. sinensis. This study exploited untargeted metabolomics and transcriptomics to uncover the differences in accumulated metabolites and expressed genes between wild and cultivated O. sinensis. Metabolomics results revealed that 368 differentially accumulated metabolites were mainly enriched in biosynthesis of amino acids, biosynthesis of plant secondary metabolites and purine nucleotide metabolism. Cultivated O. sinensis contained more amino acids and derivatives, carbohydrates and derivatives, and phenolic acids than wild O. sinensis, whereas the contents of most nucleosides and nucleotides in wild O. sinensis were significantly higher than in cultivated O. sinensis. Transcriptome analysis indicated that 4430 annotated differentially expressed genes were identified between two types. Integrated metabolomics and transcriptomics analyses suggested that IMPDH, AK, ADSS, guaA and GUK genes might be related to the synthesis of purine nucleotides and nucleosides. Our findings will provide a new insight into the molecular basis of metabolic variations of this medicinal fungus.

Metabolomics approach to assess the effect of siphonal autotomy on metabolic characteristics of razor clam Solen grandis

Autotomy appendages are fundamental evolutionary adaptations to escape predation. The siphon is an important foraging organ for bivalves. Here, we report the first demonstration of autotomy of the siphon in marine bivalves (razor clam Solen grandis) and the effect of siphonal autotomy in S. grandis on foraging and metabolic characteristics. In this study, the feeding rate and digestive enzyme activities upon siphonal autotomy in razor clams were investigated. Moreover, endogenous metabolites pre/post-autotomy of the siphon were investigated using liquid chromatography tandem-mass spectrometry (LC–MS). The feeding rate and digestive enzyme activities decreased significantly after siphonal autotomy in S. grandis (P < 0.05), suggesting that autotomy of the siphon negatively affected its foraging. These results might be related to the reduction in the foraging radius. Additionally, the effect of autotomy was investigated on a total of 34 differentially abundant metabolites, and pathway analysis indicated that 32 differentially enriched metabolic pathways were worthy of attention. Further integrated key metabolic pathway analysis showed that glycine, serine and threonine metabolism; taurine and hypotaurine metabolism; biotin metabolism; vitamin B6 and thiamine metabolism were significantly relevant pathways in S. grandis pre/post-autotomy of the siphon. The downregulation of glycine, taurine, and hypotaurine is expected to indicate a shortage of intermediate compounds and energy in S. grandis. Therefore, to provide the required energy and materials for siphon regeneration in S. grandis, we anticipated that it would be necessary to supplement these as exogenous metabolites from the daily diet.

Stage- and Rearing-Dependent Metabolomics Profiling of Ophiocordyceps sinensis and Its Pipeline Products

Cordyceps, a parasitic complex of the fungus Ophiocordyceps sinensis (Berk.) (Hypocreales: Ophiocordycipitaceae) and the ghost moth Thitarodes (Lepidoptera: Hepialidae), is a historical ethnopharmacological commodity in China. Recently, artificial cultivation of Chinese cordyceps has been established to supplement the dwindling natural resources. However, much is unknown between the natural and cultivated products in terms of nutritional aspect, which may provide essential information for quality evaluation. The current study aims to determine the metabolic profiles of 17 treatments from 3 sample groups including O. sinensis fungus, Thitarodes insect and cordyceps complex, using Gas Chromatography - Quadrupole Time-of-Flight Mass Spectrometry. A total of 98 metabolites were detected, with 90 of them varying in concentrations among groups. The tested groups could be separated, except that fungal fruiting body was clustered into the same group as Chinese cordyceps. The main distinguishing factors for the groups studied were the 24 metabolites involved in numerous different metabolic pathways. In conclusion, metabolomics of O. sinensis and its related products were determined mainly by the fruiting bodies other than culture methods. Our results suggest that artificially cultured fruiting bodies and cordyceps may share indistinguishable metabolic functions as the natural ones.

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

Background

Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica.

Results

To investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations.

Conclusions

The genomic characterization of five yeast strains isolated from N. vespilloides resulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07597-z.