Mixtures of bacterial genomic DNA were extracted using SepaGene (Sanko Junyaku, Tokyo, Japan) according to the manufacturer’s instructions. After samples were treated with 100 µg ml−1 ribonuclease (DNase-free) solution (Nippon Gene, Tokyo, Japan) in TE buffer (Nippon Gene, pH 8.0) at 37°C for 30 min and stored at 4°C for 3 days, the genomic DNA was extracted using phenol/chloroform method and recovered by ethanol precipitation.
A DNA library of approximately 600-bp was prepared using a genomic DNA sample prep kit (Illumina, San Diego, CA, USA), and DNA clusters were generated on a slide using a cluster generation kit (ver. 2) in the Illumina cluster station according to the manufacturer’s instructions. To obtain approximately 1×107 clusters per lane, the general procedure as described in the standard recipe was employed in the following order: template hybridization, isothermal amplification, linearization, blocking, denaturation, and hybridization of the sequencing primer (Illumina). All sequencing runs for 80-mers were performed with an Illumina Genome Analyzer II (GA II) using the Illumina sequencing kit (ver. 3). Fluorescent images were analyzed using the Illumina base-calling pipeline 1.5.0 to obtain FASTQ-formatted sequence data.
A DNA library of approximately 600-bp was prepared using a genomic DNA sample prep kit (Illumina, San Diego, CA, USA), and DNA clusters were generated on a slide using a cluster generation kit (ver. 2) in the Illumina cluster station according to the manufacturer’s instructions. To obtain approximately 1×107 clusters per lane, the general procedure as described in the standard recipe was employed in the following order: template hybridization, isothermal amplification, linearization, blocking, denaturation, and hybridization of the sequencing primer (Illumina). All sequencing runs for 80-mers were performed with an Illumina Genome Analyzer II (GA II) using the Illumina sequencing kit (ver. 3). Fluorescent images were analyzed using the Illumina base-calling pipeline 1.5.0 to obtain FASTQ-formatted sequence data.