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,...

Full description

Saved in:
Bibliographic Details
Published inNucleic acids research Vol. 44; no. 10; p. e99
Main Authors Zhang, Yanming, Ji, Peifeng, Wang, Jinfeng, Zhao, Fangqing
Format Journal Article
LanguageEnglish
Published England Oxford University Press 02.06.2016
Subjects
Contig Mapping
Escherichia coli - genetics
High-Throughput Nucleotide Sequencing - methods
Humans
Metagenome
Metagenomics - methods
Methods Online
Microbiota - genetics
Phaeophyceae - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Saliva - microbiology
Online AccessGet full text

Cover

More Information
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkw165