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- Publisher Website: 10.1002/jobm.201500420
- Scopus: eid_2-s2.0-84959520253
- PMID: 26426811
- WOS: WOS:000371934800011
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Article: An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms
Title | An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms |
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Authors | |
Keywords | Paired-end sequencing Taxonomic classification Single-index V3-V4 hypervariable regions Sequencing coverage |
Issue Date | 2016 |
Citation | Journal of Basic Microbiology, 2016, v. 56, n. 3, p. 321-326 How to Cite? |
Abstract | © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. The primary 16S rRNA sequencing protocol for microbial community analysis using Illumina platforms includes a single-indexing approach that allows pooling of hundreds of samples in each sequencing run. The protocol targets the V4 hypervariable region (HVR) of 16S rRNA using 150bp paired-end (PE) sequencing. However, the latest improvement in Illumina chemistry has increased the read length up to 600bp using 300bp PE sequencing. To take advantage of the longer read length, a dual-indexing approach was previously developed for targeting different HVRs. However, due to simple working protocols, the single-index 150bp PE approach still continues to be attractive to many researchers. Here, we described an extended single-indexing protocol for 300bp PE illumina sequencing that targets the V3-V4 HVRs of 16S rRNA. The new primer set led to increased read length and alignment resolution, as well as increased richness and diversity of resulting microbial profile compared to that obtained from150bp PE protocol for V4 sequencing. The β-diversity profile also differed qualitatively and quantitatively between the two approaches. Both primer sets had high coverage rates and specificity to detect dominant phyla; however, their coverage rate with regards to the rare biosphere varied. Our data further confirms that the choice of primer is the most deterministic factor in sequencing coverage and specificity. |
Persistent Identifier | http://hdl.handle.net/10722/254561 |
ISSN | 2023 Impact Factor: 3.5 2023 SCImago Journal Rankings: 0.703 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Derakhshani, Hooman | - |
dc.contributor.author | Tun, Hein Min | - |
dc.contributor.author | Khafipour, Ehsan | - |
dc.date.accessioned | 2018-06-19T15:40:53Z | - |
dc.date.available | 2018-06-19T15:40:53Z | - |
dc.date.issued | 2016 | - |
dc.identifier.citation | Journal of Basic Microbiology, 2016, v. 56, n. 3, p. 321-326 | - |
dc.identifier.issn | 0233-111X | - |
dc.identifier.uri | http://hdl.handle.net/10722/254561 | - |
dc.description.abstract | © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. The primary 16S rRNA sequencing protocol for microbial community analysis using Illumina platforms includes a single-indexing approach that allows pooling of hundreds of samples in each sequencing run. The protocol targets the V4 hypervariable region (HVR) of 16S rRNA using 150bp paired-end (PE) sequencing. However, the latest improvement in Illumina chemistry has increased the read length up to 600bp using 300bp PE sequencing. To take advantage of the longer read length, a dual-indexing approach was previously developed for targeting different HVRs. However, due to simple working protocols, the single-index 150bp PE approach still continues to be attractive to many researchers. Here, we described an extended single-indexing protocol for 300bp PE illumina sequencing that targets the V3-V4 HVRs of 16S rRNA. The new primer set led to increased read length and alignment resolution, as well as increased richness and diversity of resulting microbial profile compared to that obtained from150bp PE protocol for V4 sequencing. The β-diversity profile also differed qualitatively and quantitatively between the two approaches. Both primer sets had high coverage rates and specificity to detect dominant phyla; however, their coverage rate with regards to the rare biosphere varied. Our data further confirms that the choice of primer is the most deterministic factor in sequencing coverage and specificity. | - |
dc.language | eng | - |
dc.relation.ispartof | Journal of Basic Microbiology | - |
dc.subject | Paired-end sequencing | - |
dc.subject | Taxonomic classification | - |
dc.subject | Single-index | - |
dc.subject | V3-V4 hypervariable regions | - |
dc.subject | Sequencing coverage | - |
dc.title | An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms | - |
dc.type | Article | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1002/jobm.201500420 | - |
dc.identifier.pmid | 26426811 | - |
dc.identifier.scopus | eid_2-s2.0-84959520253 | - |
dc.identifier.volume | 56 | - |
dc.identifier.issue | 3 | - |
dc.identifier.spage | 321 | - |
dc.identifier.epage | 326 | - |
dc.identifier.eissn | 1521-4028 | - |
dc.identifier.isi | WOS:000371934800011 | - |
dc.identifier.issnl | 0233-111X | - |