ArticleNucleic acids research2016
RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Microorganisms in Macroalgae Cultivation Ecosystems: A Systematic Review and Future Prospects Based on Bibliometric Analysis.Microorganisms · 2025Review
- Metagenomics unravel distinct taxonomic and functional diversities between terrestrial and aquatic biomes.iScience · 2024Article
- New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.Environmental science & technology · 2024Article
- Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.Biophysical reviews · 2024Review
- Unexpected absence of ribosomal protein genes from metagenome-assembled genomes.ISME communications · 2022Article
- Revealing microbial species diversity using sequence capture by hybridization.Microbial genomics · 2021Article
- High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts.Microbial genomics · 2021Article
- Phylogenetic characterization and multidrug resistance of bacteria isolated from seafood cocktails.Archives of microbiology · 2021Article
- Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria.Molecular biology reports · 2021Review
- Application of Deep Learning in Plant-Microbiota Association Analysis.Frontiers in genetics · 2021Review
- Isolation of Gram-Positive, Antibiotic-Resistant Bacteria from Tactile Mobile Phones in a Northwestern Mexican City.Journal of community health · 2020Article
- The importance of airway and lung microbiome in the critically ill.Critical care (London, England) · 2020Review
- Single-cell metagenomics: challenges and applications.Protein & cell · 2018Review
- Hybridization capture reveals microbial diversity missed using current profiling methods.Microbiome · 2018Article
- MetaSort untangles metagenome assembly by reducing microbial community complexity.Nature communications · 2017Article
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Authors and funding
4 authors.
Funding
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Abstract
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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