Metagenomics of Tetracycline-Treated Sludge

The metagenomic DNA extracted from the sludge cultured with 0 and 20 mg/L tetracycline was individually subjected to high-throughput sequencing using Illumina Hiseq 2000 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The “Index 101 PE” (Paired End sequencing, 101-bp reads and 8-bp index sequence) sequencing strategy was used for the high-throughput sequencing, which generates nearly equal amount of clean reads for each sample. A base-calling pipeline (Sequencing Control Software, Illumina, San Diego, CA, USA) was applied to process the raw fluorescent images and the call sequences. The raw reads containing three or more “N” or contaminated by adapter (>15 bp overlap) were removed, and the filtered clean reads (about 1.6 Gb per each sample) were used for further metagenomic analyses. The sequencing data were deposited in the metagenomics RAST server (MG-RAST) [43 (link)] under accession number 4494851.3 (sludge treated with 20 mg/L tetracycline) and 4494856.3 (sludge without tetracycline treatment).