## 2 Materials and Methods
### Pyrosequencing Analysis  
DNA extraction, PCR amplification, amplicon quantitation, pyrosequencing, and data analysis were developed at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) on a Roche Genome Sequencer GS-FLX Titanium platform (Roche Diagnostics, Basel, Switzerland) using MOTHUR software version 1.34 [21; 22]. DNA from fermented tea leaves was extracted using the E.Z.N.A.TM Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer's instructions. The TransGen AP221-02 kit with TransStart Fastpfu DNA polymerase (TransGen Biotech, Beijing, China) was used in PCR reactions. To analyze the taxonomic composition of the bacterial and fungal community, universal primer pairs of 27F (5\({}^{\prime}\)-AGAGTTTGATCCTGG CTCAG-3\({}^{\prime}\)) with 533R (5\({}^{\prime}\)-TTA CCG CCG CTG GCA C-3\({}^{\prime}\)), and ITS1 (5\({}^{\prime}\)-TCCGTAGGTGAACCT GCCG-3\({}^{\prime}\)) with ITS4 (5\({}^{\prime}\)-TCCCTCCGTATTGATAGC-3\({}^{\prime}\)), incorporating FLX titanium adapters, which targeted the V1-V3 region of the bacterial _165 rRNA_ gene, and the ITS region of the fungal _185 rRNA_ gene, were chosen for the amplification and subsequent pyrosequencing of the PCR products, respectively. Each PCR reaction consisted of 0.4 \(\upmu\)L Fastpfu DNA polymerase, 4 \(\upmu\)L five-fold Fastpfu Buffer, 2 \(\upmu\)L 2.5 mM dNTPs, 0.8 \(\upmu\)L of each primer, 10 ng of DNA, and ddH\({}_{2}\)O to a final concentration of 20 \(\upmu\)L. The amplification program for the bacterial _165 rRNA_ gene consisted of an initial denaturation step at 95 \({}^{\circ}\)C for 2 min. This was followed by 25 cycles, where a cycle consisted of 95 \({}^{\circ}\)C for 30 s (denaturation), 55 \({}^{\circ}\)C for 30 s (annealing), and 72 \({}^{\circ}\)C for 30 s (extension), followed by a final extension of 72 \({}^{\circ}\)C for 5 min. The amplification program for the fungal _185 rRNA_ gene consisted of an initial denaturation step at 95 \({}^{\circ}\)C for 2 min. This was followed by 30 cycles, where a cycle consisted of 95 \({}^{\circ}\)C for 30 s (denaturation), 55 \({}^{\circ}\)C for 30 s (annealing), and 72 \({}^{\circ}\)C for 30 s (extension), followed by a final extension of 72 \({}^{\circ}\)C for 5 min. All PCR products were visualized on agarose gels (2% in TBE buffer) containing ethidium bromide. For each sample, three independent PCRs were performed. The triplicate products were pooled and purified using an AxyPrep PCR Clean-up Kit (Axygen Biosciences, Avygen, CA, USA). The DNA concentration of each PCR product was determined using a Quant-iT PicoGreen double-stranded DNA assay (Invitrogen, Carlsbad, CA, USA) and was quality controlled on an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Amplicon pyrosequencing was performed from the A-end using a 454/Roche A sequencing primer kit on a Roche Genome Sequencer GS-FLX Titanium platform at Majorbio Bio-Pharm Technology Co., Ltd.  
Data preprocessing was performed mainly using MOTHUR software [21; 22]. The chimeric sequences were excluded using the chimera.uchime command with default parameters [23]. Sequences with similarities >97% were clustered into one operational taxonomic unit (OTU) using MOTHUR. The taxonomical assignment of each OTU was performed using the classify.seqs command (Naive Bayesian Classifier) against the SILVA 165 rRNA gene database (release 111) at an 80% confidence level [24; 25; 26]. Community richness and diversity indices (Chao1 estimator, abundance-based coverage estimator (ACE) and Shannon indices, respectively) and rarefaction curves were obtained using MOTHUR [27]. To compare microbial community structures based on the OTU composition across all samples, a principal component analysis (PCA) was carried out using the SPSS software package (SPSS 19.0, Chicago, IL, USA). The 454 pyrosequencing data generated for this study were submitted to the Sequence Read Archive (SRA) and are available under projects SRR1634067 and SRR1633201.