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Species-Specific Identification of Streptococcus based on DNA Marker in 16S–23S rDNA Internal Transcribed Spacer

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Abstract

Streptococcus is closely correspondent to human. The accurate species-specific identification method of Streptococcus is important for the bacteria clinical diagnosis, molecular epidemiological analysis, and microecological study. In the last decades, DNA markers are widely utilized for identification of prokaryotic species. However, 16S rDNA, the most popular bacterial DNA marker, cannot properly distinguish closely related Streptococcus species. In present study, we employed 16S–23S rRNA gene internal transcribed spacer (ITS) sequence to explore the species-specific DNA marker. We predicted the secondary structure of Streptococcus ITS sequence transcribed products. Then we identified that the specific and consensus sequences in the primary structure can be found occupying an individual subunit in the secondary structure, which explained the foundation of the mosaic-like structure of ITS. We evaluated the specificity of ITS in Streptococcus, and found that the specificity can be detected by a further analysis of a BLAST result. Then, we developed an identification procedure based on the ITS sequence. We verified the procedure by 500 ITS sequence. The accuracy rate of this procedure was 100% for Streptococcus at genus level, and 99.3% at species level. It suggested that ITS can be utilized to accurately identify Streptococcus at the species level. This work suggests that further exploration of ITS could be applied in other bacterial genera for identification and classification, which may be a useful topic for future microbiology studies.

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Acknowledgements

This work was supported by a project from the National Undergraduate Training Program for Innovation and Entrepreneurship (No. 201910055108) and by the Fundamental Research Funds for the Central Universities, Nankai University (No. 6391159).

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Authors and Affiliations

  1. College of Life Sciences, Qingdao University, Qingdao, People’s Republic of China

    Jia Yu & Yuxi Wei

  2. School of Medicine, Nankai University, Tianjin, People’s Republic of China

    Ting Zhou, Baojie Zhu, Xuerui Li & Yin Liu

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  1. Jia Yu
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  3. Baojie Zhu
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YL contributed to the study conception. All authors contributed to the study design. Material preparation, data collection, and analysis were performed by JY, TZ, and BZ. The first draft of the manuscript was written by JY and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yin Liu.

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Yu, J., Zhou, T., Zhu, B. et al. Species-Specific Identification of Streptococcus based on DNA Marker in 16S–23S rDNA Internal Transcribed Spacer. Curr Microbiol 77, 1569–1579 (2020). https://doi.org/10.1007/s00284-020-01975-8

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