Bacterial and Fungal Communities in Pu'er Tea Samples of Different Ages

Bioinformatic approaches for studying the microbiome of fermented food

High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.

Expression of citrinin biosynthesis gene in Liupao tea and effect of Penicillium citrinum on tea quality

Similar to Pu-erh tea, Liupao tea is a post-fermented tea that is produced through natural fermentation by microorganisms. Penicillium citrinum is involved in multiple production processes of Liupao tea that can produce citrinin, a secondary metabolite with renal toxicity; however, the effect of P. citrinum on the quality of Liupao tea has not been investigated yet. Citrinin production is regulated by approximately 16 biosynthesis genes. However, little is known about the genetic background of citrinin in the complex Liupao tea system. In the present study, we cultured P. citrinum on potato dextrose agar and Liupao tea powder media and analyzed the changes of its nutritional components in Liupao tea. We selected six citrinin biosynthesis genes identified in Monascus exhibiting homology and high sequence similarity to those in P. citrinum and further analyzed the expression of citrinin biosynthesis genes in Liupao tea and the changes in citrinin yield. The results showed that the changes in nutritional components of Liupao tea were closely related to the growth and metabolism of P. citrinum and the quality of the tea. Decreases in the contents of soluble sugars (from 10.29% to 9.58%), soluble pectins (from 3.71% to 3.13%), free amino acids (from 3.84% to 3.14%), and tea polyphenols (from 22.84% to 18.78%) were noted. The Spearman's correlation analysis indicated that P. citrinum growth can improve the tea quality to some extent. Quantitative real-time PCR demonstrated that ctnA gene was a positive regulator of citrinin production regardless of the culture medium used. ctnA and orf5 expressions greatly influenced the metabolism of citrinin by P. citrinum in Liupao tea. In conclusion, the citrinin biosynthesis genes, ctnA and orf5, may be the promising targets for developing strategies to control P. citrinum infection and citrinin biosynthesis in Liupao tea.

Discrimination and characterization of the volatile profiles of five Fu brick teas from different manufacturing regions by using HS-SPME/GC-MS and HS-GC-IMS

Although aroma is one of the most essential factors determining the quality of Fu brick tea (FBT), the aroma profiles of FBTs from different manufacturing areas are rarely investigated. The aroma profiles of FBTs manufactured in five typical provinces of China were comprehensively analyzed on the basis of headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS), headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), sensory evaluation, odor activity value (OAV), and relative odor activity value (ROAV). HS-GC-IMS and HS-SPME-GC-MS identified 63 and 93 volatile organic compounds (VOCs), respectively. Multivariate statistical analysis indicated that the FBTs from different production regions had remarkably varied aromas. HS-SPME-GC-MS revealed that 27 VOCs (OAV >1) contributed to the overall aroma of the samples, of which 15 key differential compounds can effectively distinguish the aroma profiles of different FBTs. FBT from Shaanxi manifested a strong floral and fruity aroma; that from Hunan had a floral, grassy, and pine-woody aroma; that from Guizhou presented a grassy and herbal aroma; that from Guangxi exhibited a sweet, floral, and minty aroma; and that from Zhejiang possessed various fruit flavors and floral fragrance. OAV analysis identified the biomarkers responsible for the variation in the aroma characteristics of diverse FBTs. These biomarkers included linalool, 6-methyl-5-hepten-2-one, α-ionone, hexanal, and ethyl hexanoate. Sensory evaluation demonstrated that the infusion color and aroma of FBT samples from different provinces also greatly varied. Network correlation analysis revealed that Aspergillus and Eurotium were the crucial microorganisms for the metabolism and formation of VOCs. These findings provide new insight into the VOCs and fragrance features of FBTs produced in different regions of China.

A Correlation Between Pericarpium Citri Reticulatae Volatile Components and the Change of the Coexisting Microbial Population Structure Caused by Environmental Factors During Aging

Pericarpium Citri Reticulatae (PCR) is a natural citrus by-product with beneficial health and nutritive properties that is used widely in food and is an ingredient in traditional Chinese medicine. PCR improves gradually with aging. However, the present research has not yet revealed the reasons for this. Some data prove the important role of microorganisms in the quality of tobacco and fermented tea with the time of the aging of these foods. Our studies further proved that the coexisting Aspergillus niger plays an important role in the change of flavonoids and volatile oil in PCR during this process. Therefore, we put forward that longer storage is better for PCR and is highly correlated with the change of the coexisting microbial population structure caused by environmental factors. Samples of PCR aged in Beijing, Sichuan, Guangdong, and Yunnan were collected at different time points. Using GC/MS and high throughput 16S rDNA and ITS sequencing techniques, massive changes in volatile profile and microbial communities were observed during aging. Spearman correlation analysis indicated that Exobasidium, Xeromyces, Pseudocercospora, Russula, Aspergillus, Herbaspirillum, Sphingomonas, and Streptococcus, which are the dominant microbial genera in Sichuan and Guangdong showed strong connections with volatile components of chemical markers. It was preliminarily verified that the changes of volatile components for PCR are highly correlated with the change of the coexisting microbial population structure caused by environmental factors, providing a new idea for the research on the aging mechanism of PCR and key influencing factors of aging quality.

Evaluation of Mycoflora and Citrinin Occurrence in Chinese Liupao Tea

Citrinin (CIT), a known nephrotoxic mycotoxin, is mainly produced by Penicillium, Aspergillus, and Monascus species. It is a natural contaminant in cereal grains, foods, and feedstuff. Liupao tea (or Liubao tea) is a typical Chinese dark tea obtained via indigenous tea fermentation facilitated by microorganisms. Certain fungi present in Liupao tea that may produce CIT are a potential threat to consumer health. In the present study, various potential toxigenic mycoflora and the natural occurrence of CIT in Liupao tea were surveyed via the culture-dependent method, high performance liquid chromatography-fluorescence detection (HPLC-FLD), and ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Total mold counts ranged from 3.5 × 10² CFU/g to 2.1 × 10⁶ CFU/g tea in 28 tea samples. A total of 218 fungal isolates belonging to five genera and 23 species were identified. Some of these strains, such as Aspergillus ochraceus, Aspergillus oryzae, Penicillium citrinum, and Penicillium chrysogenum, may potentially be a CIT-producing species. In addition, 32.7% of 113 Liupao tea samples were contaminated with CIT at concentrations ranging from 7.8 to 206.1 μg/kg. These CIT concentrations in Liupao tea are chiefly attributed to climatic conditions and water activity during storage that favor fungal proliferation and mycotoxin production. However, CIT could not be detected in Liupao tea stored for over 10 years. These results provide the first information about the potential toxigenic mycoflora and natural occurrence of CIT in Liupao tea. Therefore, storage conditions and fungal community must be monitored to ensure the quality of Liupao tea.

Correlation analysis between filamentous fungi and chemical compositions in a pu-erh type tea after a long-term storage

Storage environment caused the difference between Jinhua Pu-erh tea (JPT) and General Pu-erh tea. In this study, fungal flora and chemical compositions were analyzed. The results showed that storage environment caused significant (p < .05) differences of theaflavins (TF), theabrownins (TB), tea polyphenols (TP), and water-soluble sugars (WSS), and a highly significant (p < .01) difference of thearubigins (TR). Aspergillus niger, Aspergillus pallidofulvus, Aspergillus sesamicola, Penicillium manginii, and Aspergillus tamarii were isolated from Pu-erh teas and identified based on colony characteristics and ITS, β-tubulin, and calmodulin gene sequences, respectively. A. pallidofulvus, A. sesamicola, and P. manginii were dominant fungi in JPT and generated macroscopic yellow cleistothecia after a long-term storage. Correlation analysis showed that dominant fungi exhibited significantly (p < .05 or p < .01) positive or negative corrections with TF, TB, TP, WSS, TR, and gallic acid. This study revealed dominant fungi including A. pallidofulvus, A. sesamicola, and P. manginii and their effects on given chemical compositions.

Isolation, characterization and application of theophylline-degrading Aspergillus fungi

Background

Caffeine, theobromine and theophylline are main purine alkaloid in tea. Theophylline is the downstream metabolite and it remains at a very low level in Camellia sinensis. In our previous study, Aspergillus sydowii could convert caffeine into theophylline in solid-state fermentation of pu-erh tea through N-demethylation. In this study, tea-derived fungi caused theophylline degradation in the solid-state fermentation. The purpose of this study is identify and isolate theophylline-degrading fungi and investigate their application in production of methylxanthines with theophylline as feedstock through microbial conversion.

Results

Seven tea-derived fungi were collected and identified by ITS, β-tubulin and calmodulin gene sequences, Aspergillus ustus, Aspergillus tamarii, Aspergillus niger and A. sydowii associated with solid-state fermentation of pu-erh tea have shown ability to degrade theophylline in liquid culture. Particularly, A. ustus and A. tamarii could degrade theophylline highly significantly (p < 0.01). 1,3-dimethyluric acid, 3-methylxanthine, 3-methyluric acid, xanthine and uric acid were detected consecutively by HPLC in A. ustus and A. tamarii, respectively. The data from absolute quantification analysis suggested that 3-methylxanthine and xanthine were the main degraded metabolites in A. ustus and A. tamarii, respectively. 129.48 ± 5.81 mg/L of 3-methylxanthine and 159.11 ± 10.8 mg/L of xanthine were produced by A. ustus and A. tamarii in 300 mg/L of theophylline liquid medium, respectively.

Conclusions

For the first time, we confirmed that isolated A. ustus, A. tamarii degrade theophylline through N-demethylation and oxidation. We were able to biologically produce 3-methylxanthine and xanthine efficiently from theophylline through a new microbial synthesis platform with A. ustus and A. tamarii as appropriate starter strains.

Metabolomics Based on UHPLC-Orbitrap-MS and Global Natural Product Social Molecular Networking Reveals Effects of Time Scale and Environment of Storage on the Metabolites and Taste Quality of Raw Pu-erh Tea

Raw Pu-erh tea (RPT) needs ageing before drinking. However, the influence from environment and time of storage on chemical profile and flavor of RPT is unclear. In this study, the RPTs stored in wet-hot or dry-cold environment for 1-9 years were assessed using metabolomics based on UHPLC-Orbitrap-MS and global natural product social (GNPS) feature-based molecular networking as well as electronic tongue measurement. The results exhibited that the chemical profiles of RPTs were similar at an early stage but started to differentiate from each other at the 5th and the 7th year in wet-hot and dry-cold environments. The discriminating features including N-ethyl-2-pyrrolidinone-substituted flavan-3-ols (flavoalkaloids), unsaturated fatty acids, lysophosphatidylcholines, flavan-3-ols, amino acids, and flavonol-O-glycosides among the three chemical profiles were discovered and analyzed by means of multivariate statistics, GNPS multilibraries matching, and SIRIUS calculation. The metabolomic data were consistent with the results obtained through electronic tongue measurement.

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation

Xiaguan Tuo Tea is largely consumed by the Chinese, but there is little research into the microbial diversity and component changes during the fermentation of this tea. In this study, we first used fluorescence in situ hybridization (FISH), next-generation sequencing (NGS) and chemical analysis methods to determine the microbial abundance and diversity and the chemical composition during fermentation. The FISH results showed that the total number of microorganisms ranges from 2.3×10² to 4.0×10⁸ cells per gram of sample during fermentation and is mainly dominated by fungi. In the early fermentation stages, molds are dominant (0.6×10²~2.8×10⁶ cells/g, 0~35 d). However, in the late stages of fermentation, yeasts are dominant (3.6×10⁴~9.6×10⁶ cells/g, 35~56 d). The bacteria have little effect during the fermentation of tea (10²~10³ cells/g, <1% of fungus values). Of these fungi, A. niger (Aspergillus niger) and B. adeninivorans (Blastobotrys adeninivorans) are identified as the two most common strains, based on Next-generation Sequencing (NGS) analysis. Peak diversity in tea was observed at day 35 of fermentation (Shannon–Weaver index: 1.195857), and lower diversity was observed on days 6 and 56 of fermentation (Shannon–Weaver index 0.860589 and 1.119106, respectively). During the microbial fermentation, compared to the unfermented tea, the tea polyphenol content decreased by 54%, and the caffeine content increased by 59%. Theanine and free amino acid contents were reduced during fermentation by 81.1 and 92.85%, respectively.

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis

Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption.

Characterization of thermophilic fungal community associated with pile fermentation of Pu-erh tea

This study aimed to characterize the thermophilic fungi in pile-fermentation process of Pu-erh tea. Physicochemical analyses showed that the high temperature and low pH provided optimal conditions for propagation of fungi. A number of fungi, including Blastobotrys adeninivorans, Thermomyces lanuginosus, Rasamsonia emersonii, Aspergillus fumigatus, Rhizomucor pusillus, Rasamsonia byssochlamydoides, Rasamsonia cylindrospora, Aspergillus tubingensis, Aspergillus niger, Candida tropicalis and Fusarium graminearum were isolated as thermophilic fungi under combination of high temperature and acid culture conditions from Pu-erh tea pile-fermentation. The fungal communities were analyzed by PCR-DGGE. Results revealed that those fungi are closely related to Debaryomyces hansenii, Cladosporium cladosporioides, A. tubingensis, R. emersonii, R. pusillus, A. fumigatus and A. niger, and the last four presented as dominant species in the pile process. These four preponderant thermophilic fungi reached the order of magnitude of 10(7), 10(7), 10(7) and 10(6)copies/g dry tea, respectively, measured by real-time quantitative PCR (q-PCR). The results indicate that the thermophilic fungi play an important role in Pu-erh tea pile fermentation.

Effects of aging on the phytochemical profile and antioxidative activity of Pericarpium Citri Reticulatae ‘Chachiensis’

PCR-Chachiensis stored long-term exhibits higher total phenolics, flavonoid content and superior antioxidant activity, which provide additional health benefits during aging.