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RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately,...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889936/ https://www.ncbi.nlm.nih.gov/pubmed/26984526 http://dx.doi.org/10.1093/nar/gkw165 |
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author | Zhang, Yanming Ji, Peifeng Wang, Jinfeng Zhao, Fangqing |
author_facet | Zhang, Yanming Ji, Peifeng Wang, Jinfeng Zhao, Fangqing |
author_sort | Zhang, Yanming |
collection | PubMed |
description | 16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities. |
format | Online Article Text |
id | pubmed-4889936 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48899362016-06-06 RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes Zhang, Yanming Ji, Peifeng Wang, Jinfeng Zhao, Fangqing Nucleic Acids Res Methods Online 16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities. Oxford University Press 2016-06-02 2016-03-16 /pmc/articles/PMC4889936/ /pubmed/26984526 http://dx.doi.org/10.1093/nar/gkw165 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Online Zhang, Yanming Ji, Peifeng Wang, Jinfeng Zhao, Fangqing RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title | RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title_full | RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title_fullStr | RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title_full_unstemmed | RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title_short | RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes |
title_sort | ribofr-seq: a novel approach to linking 16s rrna amplicon profiles to metagenomes |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889936/ https://www.ncbi.nlm.nih.gov/pubmed/26984526 http://dx.doi.org/10.1093/nar/gkw165 |
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