Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota

Meng,Fanjing; Chen,Tingtao; Wang,Xin; Wang,Xiaolei; Wei,Hua; Tian,Puyuan; Wang,Huan; Zhao,Xiaoxiao; Shen,Liang; Xin,Hongbo

doi:10.3892/mmr.2017.7849

Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota

Authors:
- Fanjing Meng
- Tingtao Chen
- Xin Wang
- Xiaolei Wang
- Hua Wei
- Puyuan Tian
- Huan Wang
- Xiaoxiao Zhao
- Liang Shen
- Hongbo Xin
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Affiliations: Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China, State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, P.R. China, Department of Obstetrics and Gynaecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250012, P.R. China
Published online on: October 20, 2017 https://doi.org/10.3892/mmr.2017.7849
Pages: 408-413

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Abstract

Next generation sequencing provides an excellent platform to explore microbiota in any given environment, and little work is required to evaluate the accuracy and sensitivity of high‑throughput sequencing technology. In the present study, a known microbiota containing Escherichia coli, Lactobacillus plantarum, Streptococcus thermophilus, Bifidobacterium bifidum, Bacillus subtilis, Enterococcus faecalis and Salmonella typhimurium was used to evaluate the high‑throughput sequencing technology. The results suggested that there were 122.7 operational taxonomic units (OTUs) in all groups, which is 17.5‑fold (the whole OTU number/the actual bacterial number) greater compared with the actual microbial number in each group, and the Venn method indicated that only 46.38% (64/138), 58.70% (81/138), 86.13% (118/137), 83.57% (117/140) and 89.29% (125/140) of the common OTUs were identified in groups A, B, C, D and E, of which the majority of OTUs did not belong to known bacteria. In addition, the DNA extraction and amplification efficiency failed to identify bacteria at the phylum, class, order, family, genus and species levels, which may further increase false information of microbial analysis. In conclusion, the present study provided basic datato investigate the potential drawbacks of high‑throughput sequencing technology, which will help researchers to avoid exaggerating the bacterial number when this technology is applied to study microbiota in particular environments.

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