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Comparison of the Performance of MiSeq and HiSeq 2500 in a Microbiome Study

Microbiology and Biotechnology Letters 2020년 48권 4호 p.574 ~ 581
나희삼, Yu Yeuni, 김시영, 이재형, 정진,
소속 상세정보
나희삼 ( Na Hee-Sam ) - Pusan National University School of Dentistry Department of Oral Microbiology
 ( Yu Yeuni ) - Pusan National University Interdisplinary Program of Genomic Science
김시영 ( Kim Si-Yeong ) - Pusan National University School of Dentistry Department of Oral Microbiology
이재형 ( Lee Jae-Hyung ) - Kyung Hee University School of Dentistry Department of Oral Microbiology
정진 ( Chung Jin ) - Pusan National University School of Dentistry Department of Oral Microbiology

Abstract


Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is commonly used to analyze the microbiome due to its relatively long read length. However, recently, Illumina introduced the 250x2 chip for HiSeq 2500. The purpose of this study was to compare the performance of MiSeq and HiSeq in the context of oral microbiome samples. The MiSeq Reagent Kit V3 and the HiSeq Rapid SBS Kit V2 were used for MiSeq and HiSeq 2500 analyses, respectively. Total read count, read quality score, relative bacterial abundance, community diversity, and relative abundance correlation were analyzed. HiSeq produced significantly more read sequences and assigned taxa compared to MiSeq. Conversely, community diversity was similar in the context of MiSeq and HiSeq. However, depending on the relative abundance, the correlation between the two platforms differed. The correlation between HiSeq and MiSeq sequencing data for highly abundant taxa (> 2%), low abundant taxa (2?0.2%), and rare taxa (0.2% >) was 0.994, 0.860, and 0.416, respectively. Therefore, HiSeq 2500 may also be compatible for microbiome studies. Importantly, the HiSeq platform may allow a high-resolution massive parallel sequencing for the detection of rare taxa.

키워드

Microbiome; MiSeq; HiSeq; next generation sequencing

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