Fermented foods play important roles in diets worldwide and account for approximately one-third of all foods and beverages consumed. To date, traditional fermentation has used spontaneous fermentation. The microbiome in fermentation has direct impacts on the quality and safety of fermented foods and contributes to the preservation of traditional methods. Here, we used an integrated meta-omics approach to study the microbiome in the fermentation of pu-erh tea, which is a well-known Chinese fermented food with a special flavor and healthful benefits. This study advanced the knowledge of microbiota, metabolites, and enzymes in the fermentation of pu-erh tea. These novel insights shed light onto the complex microbiome in pu-erh fermentation and highlight the power of integrated meta-omics approaches in understanding the microbiome in food fermentation ecosystems.

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Bursaphelenchus xylophilus is the causative agent of pine wilt disease which has caused huge economic losses in many countries. It has been reported that two forms of pine wood nematodes existed in its native region, i.e., with strong virulence and weak virulence. However, little is known about the molecular differences between the two forms. To better understand their molecular variations, transcriptome and genome sequences of three strongly virulent and one weakly virulent strains were analyzed. We found 238 transcripts and 84 exons which showed notable changes between the two virulent forms. Functional analyses of both differentially expressed transcripts and exons indicated that different virulence strains showed dissimilar nematode growth, reproduction, and oxidoreductase activities. In addition, we also detected a small number of exon-skipping events in B. xylophilus. Meanwhile, 117 SNPs were identified as potential genetic markers in distinguishing the two forms. Four of them were further proved to have undergone allele specific expressions and possibly interrupted the target site of evolutionary conserved B. xylophilus miR-47. These particular SNPs were experimentally verified by including eight additional strains to ensure the validity of our sequencing results. These results could help researchers to better diagnose nematode species with different virulence and facilitate the control of pine wilt disease.

Although the pathway and transcription factor regulation of anthocyanin biosynthesis in tea plants [Camellia sinensis (L.) O. Ktze] are known, post-transcriptional regulation mechanisms involved in anthocyanin accumulation have not been comprehensively studied. We obtained the full-length transcriptome of a purple cultivar ('Zijuan') and a normal green cultivar ('Yunkang 10#') of C. sinensis var. asssamica (Masters) showing different accumulation of anthocyanins and catechins through PacBio isoform sequencing (Iso-Seq). In total, 577,557 mapped full-length cDNAs were obtained, and 2,600 average-length gene isoforms were identified in both cultivars. After gene annotations and pathway predictions, we found that 98 key genes in anthocyanin biosynthesis pathways could have undergone alternative splicing (AS) events, and identified a total of 238 isoforms involved in anthocyanin biosynthesis. We verified expression of the C4H, CHS, FLS, CCOM, F3'5'H, LAR, PAL, CCR, CYP73A13, UDP75L12, UDP78A15/UFGT, UDP94P1, GL3, MYB113, ANR, ANS, F3H, 4CL1, CYP98A3/C3H, CHI, DFR genes and their AS transcripts using qRT-PCR. Correlation analysis of anthocyanin biosynthesis and gene expression results revealed that C4H1, FLS1, PAL2, CCR2, UDP75L122 and MYB113-1 are crucial AS transcripts for regulating anthocyanin biosynthesis in C. sinensis var. assamica. Our results reveal post-transcriptional regulation of anthocyanin biosynthesis in tea plants, and provide more new insights into the regulation of secondary metabolism.

A high performance liquid chromatography method for simultaneous detection of 20 bioactive components in tea extractsTea is the second most widely consumed beverage and contains various bioactive compounds. A simple method to analyze these compounds is of great scientific and commercial interest. In this work, a 30 min HPLC method was developed using a simple gradient elution system, and the mobile phases and elution gradients were optimized. This method separated 17 polyphenols and three alkaloid compounds in tea extracts, including catechins, alkaloids, phenolic acids, flavonols, and flavone, which are responsible for the bioactivity and flavor of tea. Excellent linearity was observed for all standard calibration curves, and correlation coefficients were above 0.9994. Heatmap analysis demonstrated significant separation between green, black, and pu-erh tea samples. The method described here is accurate and sensitive enough for the determination of active components in tea and could potentially be applied to other food products for the comprehensive investigation of their quality.

Tannase (E.C. 3.1.1.20) is hypothesized to be involved in the metabolism of gallates and gallic acid (GA) in pu-erh tea fermentation. In this work, we measured tannase in Aspergillus niger fermented tea leaves and confirmed the production of fungal tannase during pu-erh tea fermentation. A decrease in catechin and theaflavin gallates and a significant increase in GA content and the relative peak areas of ethyl gallate, procyanidin A2, procyanidin B2, procyanidin B3, catechin-catechin-catechin, epiafzelechin, and epicatechin-epiafzelechin [variable importance in the projection (VIP) > 1.0, p < 0.05, and fold change (FC) > 1.5] were observed using high performance liquid chromatography (HPLC) and metabolomics analysis of tea leaves fermented or hydrolyzed by tannase. In vitro assays showed that hydrolysis by tannase or polymerization of catechins increased the antioxidant activity of tea leaves. In summary, we identified a metabolic pathway for gallates and their derivatives in tea leaves hydrolyzed by tannase as well as associated changes in gallate and GA concentrations caused by fungal tannase during pu-erh tea fermentation.

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Flavonoids are rich in tea plants (Camellia sinensis), and responsible for the flavor and healthful benefits of tea beverage. The anthocyanin levels in the purple tender shoots are higher than in the general green leaves of tea plant, which provide special materials to search metabolic mechanisms of flavonoid enrichment in plant. In this work, flavonoid differences between purple and green shoots from tea cultivars ‘Zijuan’ (ZJ) and ‘Yunkang10’ (YK-10) were investigated through metabolomic analysis, and mechanisms for their difference were surveyed by comparative transcriptomic and proteomic analysis. Levels of 34 flavonoids were different between ZJ and YK-10 shoots. Among them, eight and six were marker metabolites in ZJ and YK-10, respectively. The differentially expressed genes (DEGs), proteins (DEPs) and different-level metabolites (DLMs) between ZJ and YK-10 were researched, respectively; and interactions including DEG-DLM, DEP-DLM, DEG-DEP and DEG-DEP-DLM were analyzed; the contents of 18 characteristic flavonoids in tea leaves and expressions of 34 flavonoid metabolic genes were measured to verify the omics results. Integrated above analyses, a proposed model of flavonoids biosynthesis in tea shoots were established. The differential expression of the leucoanthocyanidin reductase (LAR), anthocyanidin synthase (ANS), anthocyanidin reductase (ANR), UDPG-flavonoid glucosyltransferase (UGT) 75L12 and 94P1 at gene level, and the ANS, ANR and UGT78A15 at protein level, were closely associated with differences in flavonoids between ZJ and YK-10 shoot. Together, this study provides new information on the flavonoid accumulation mechanism in tea plant.