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

Yu, Jia; Zhou, Ting; Zhu, Baojie; Wei, Yuxi; Yin, Liang

doi:10.1007/s00284-020-01975-8

Cited by 4 publications

(4 citation statements)

References 40 publications

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“…All subsequences were aligned with the WSs of each genome using BLAST with the default setting on the NCBI ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ). Further analysis of BLAST results were performed [ 31 , 39 ]. The Max Score was used as it covers the comprehensive results of the E value and other results.…”

Section: Methodsmentioning

confidence: 99%

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Species-specific identification of Pseudomonas based on 16S–23S rRNA gene internal transcribed spacer (ITS) and its combined application with next-generation sequencing

Yin

et al. 2022

BMC Microbiol

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Background Pseudomonas species are widely distributed in the human body, animals, plants, soil, fresh water, seawater, etc. Pseudomonas aeruginosa is one of the main pathogens involved in nosocomial infections. It can cause endocarditis, empyema, meningitis, septicaemia and even death. However, the Pseudomonas classification system is currently inadequate and not well established. Results In this study, the whole genomes of 103 Pseudomonas strains belonging to 62 species available in GenBank were collected and the specificity of the 16S–23S ribosomal RNA internal transcribed spacer (ITS) sequence was analysed. Secondary structures of ITS transcripts determining where the diversity bases were located were predicted. The alignment results using BLAST indicated that the ITS sequence is specific for most species in the genus. The remaining species were identified by additional frequency analyses based on BLAST results. A double-blind experiment where 200 ITS sequences were randomly selected indicated that this method could identify Pseudomonas species with 100% sensitivity and specificity. In addition, we applied a universal primer to amplify the Pseudomonas ITS of DNA extracts from fish samples with next-generation sequencing. The ITS analysis results were utilized to species-specifically identify the proportion of Pseudomonas species in the samples. Conclusions The present study developed a species-specific method identification and classification of Pseudomonas based on ITS sequences combined NGS. The method showed its potential application in other genera.

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Section: Methodsmentioning

confidence: 99%

“…cgi). Further analysis of BLAST results were performed [31,39]. The Max Score was used as it covers the comprehensive results of the E value and other results.…”

Section: Its Sequence Specificity Analysismentioning

confidence: 99%

Species-specific identification of Pseudomonas based on 16S–23S rRNA gene internal transcribed spacer (ITS) and its combined application with next-generation sequencing

Yin

et al. 2022

BMC Microbiol

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“…Pourahmad et al (2019) performed sequence analysis of the mycobacterial 16S-23S ITS region to determine aquatic mycobacteria species, reporting effectiveness of this marker. In another study, Yu et al (2020) evaluated the species specificity of ITS. For this purpose, they improved a determination method based on 500 ITS sequences.…”

Section: Its (Internal Transcribed Spacer)mentioning

confidence: 99%

“…Moreover, development of EST-SSR markers have been also studied in Indian mulberry (Thumilan et al, 2016), Lycium barbarum (Chen et al, 2017), Bletilla striata (Xu et al, 2018), Lilium (Biswas et al, 2018, Chinese Hawthorn (Ma et al, 2019) and opium poppy (Vašek et al, 2020). In addition to plants, these markers are also used for animal (Li et al, 2020;Silva Junior et al, 2020) and human (Pai et al, 2016).…”

Section: Ssr (Simple Sequence Repeats)mentioning

confidence: 99%