Illumina MiSeq sequencing of SAMD00066089
Each of the 121 Samples was gut metagenome isolated from Litopenaeus Vannamei. Gut bacteria DNA was extracted using the FAST DNA Spin kit (MO BIO Laboratories, Carlsbad, CA, USA) according to the manufacturer???s protocols.
The obtained gut bacteria PCR products were pooled after purification with AMPure XP Kit (Beckman Coulter) and the pooledlibrary was subjected to an Illumina Miseq run with the 2 x 300 cyclesequencing kit (version 3). Triplicated polymerase chain reaction (PCR) amplicons were pooled together. Polymerase chain reaction amplicons were purified using a PCR fragment purification kit (Takara, Japan) and quantified using a Quant-It Pico Green kit (Invitrogen, USA) with a Qubit fluorometer (Life Technologies, USA). An equimolar amount of PCR amplicons were combined into one pooled sample and submitted to Novogene Beijing for Illumina paired-end (PE) library preparation, cluster generation and 250 bp PE sequencing on an Illumina MiSeq machine. Sequence data were filtered using QIIME (version 1.7.0) (Caporaso et al., 2010) and removed UCHIME using mothur software (version 1.31.2) (Schloss PD et al., 2009; Edgar RC et al., 2011). Raw FASTQ files were de-multiplexed with QIMME v1.7.0 (Caporaso et al., 2010), and the paired reads were joined with FLASH (fast length adjustment of short reads) using default setting (Magoc?? and Salzberg, 2011). The joined pairs were then quality filtered and analysed with QIMME.