IADR Abstract Archives
Comparison between MiSeq and HiSeq 2500 for Microbiome analysis
Objectives: Next generation sequencing is commonly used to characterize the structure of oral microbiome in both healthy subjects as well as in patients with various oral diseases that are considered to be influenced by oral bacteria. MiSeq has been most commonly used the analyze oral microbiome due to its relatively long read length. Illumina has also introduced 250x2 chip for HiSeq 2500. The purpose of this study is to compare performance between MiSeq and HiSeq platform for microbiome analysis.
Methods: Oral microbiome samples from 20 subjects were collected from supragingiva using microbrush. DNA isolation kit was used to extract DNA according to manufacture’s instruction. MiSeq Reagent Kit V3 and HiSeq Rapid SBS Kit V2 was respectively used for MiSeq and HiSeq 2500 analysis. Total read count, Q30% as well as each data quality for read 1 and read 2 was compared between each samples. Also, taxonomy assignment and community diversity was compared.
Results: Read length for MiSeq was significantly longer compared to HiSeq 2500 (500 vs 600 bps). MiSeq produced total of 6.27 x 10(6) reads and 3.14x10(5) ± 3.00 x10(4) reads for each sample while HiSeq produced total of 1.17 x 10(7) reads and 5.86 x10(5) ± 7.40x10(4) reads for each sample. Average Q20 was 91.27 ± 2.06 (MiSeq) and 92.42 ± 0.48 (HiSeq). Average Q30 was 82.45 ± 3.14 (MiSeq) and 86.75 ± 0.82 (HiSeq). When each samples were analyzed for the data quality, Q30% score between 250 to 300 bp for both read 1 and read 2 showed dramatic decrease while there was no such decrease in HiSeq reads. When overall taxonomic assignment and community diversity was compared, both platforms showed similar outcomes.
Conclusions: Although MiSeq is most commonly used for microbiome study, HiSeq 2500 may also be compatible for microbiome study.
Methods: Oral microbiome samples from 20 subjects were collected from supragingiva using microbrush. DNA isolation kit was used to extract DNA according to manufacture’s instruction. MiSeq Reagent Kit V3 and HiSeq Rapid SBS Kit V2 was respectively used for MiSeq and HiSeq 2500 analysis. Total read count, Q30% as well as each data quality for read 1 and read 2 was compared between each samples. Also, taxonomy assignment and community diversity was compared.
Results: Read length for MiSeq was significantly longer compared to HiSeq 2500 (500 vs 600 bps). MiSeq produced total of 6.27 x 10(6) reads and 3.14x10(5) ± 3.00 x10(4) reads for each sample while HiSeq produced total of 1.17 x 10(7) reads and 5.86 x10(5) ± 7.40x10(4) reads for each sample. Average Q20 was 91.27 ± 2.06 (MiSeq) and 92.42 ± 0.48 (HiSeq). Average Q30 was 82.45 ± 3.14 (MiSeq) and 86.75 ± 0.82 (HiSeq). When each samples were analyzed for the data quality, Q30% score between 250 to 300 bp for both read 1 and read 2 showed dramatic decrease while there was no such decrease in HiSeq reads. When overall taxonomic assignment and community diversity was compared, both platforms showed similar outcomes.
Conclusions: Although MiSeq is most commonly used for microbiome study, HiSeq 2500 may also be compatible for microbiome study.