Unravelling the community structure and metabolic potentials of a traditional rice beer starter ‘emao’ through metagenomics analysis. Metagenomics study on the rice beer starter 'emao'

Metagenomic DNA of a pooled-emao sample was isolated using MoBio DNA isolation kit (QIAGEN, Cat. No. 12888-100). The quality of the DNA was confirmed in Qubit Fluorometer and agarose gel electrophoresis before the library preparation. The Genomic DNA was fragmented using Covaris M220 for 500bp, and the library was prepared using NEBNext Ultra DNA Library Prep Kit. The library quality was checked using Agilent Tapestation 2200. The quantity was estimated using Qubit 2.0. The libraries were sequenced in the HiSeq 2500 platform for 2x250bp read length generating the required data. The FASTQ files generated by the Illumina HiSeq platform were trimmed with Cutadapt (Version 1.8.1) to remove the adapters. The forward and reverse DNA sequences in fastq format were submitted in MAPLE Submission Data Maker (MSDM) to translate the quality DNA sequences into amino acid (AA) sequences. The AA sequences so obtained were analyzed in Genomaple (ver. 2.3.2) for KEGG orthology (KO) gene assignment and subsequent metabolic potential prediction. Carbohydrate-active enzymes (CAZymes) and biofuel-producing enzymes (BPZymes) were identified doing homology search against dbCAN and BioFuelDB, respectively. The ribosomal protein sequences were retrieved from the Genomaple result for further species level taxonomic binning after homology search against NCBI protein database.