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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,...

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Detalles Bibliográficos
Autores principales: Zhang, Yanming, Ji, Peifeng, Wang, Jinfeng, Zhao, Fangqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
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.
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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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