ArticleNucleic acids research2019
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 345 papers, 1 of them a synthesis that pooled it.
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Who cites it
345 citing papers in PubMed, 1 synthesis or guideline pooled it, 662 citations in OpenAlex.
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- A human milk oligosaccharide alters the microbiome, circulating hormones, and metabolites in a randomized controlled trial of older adults.Cell reports. Medicine · 2025Trial
- Early risk stratification of late-onset sepsis in very preterm infants by intestinal microbiota profiling: a multicenter case-control validation study.Gut microbes · 2026Article
- Environmental variables associated with Arbuscular Mycorrhizal Fungi diversity in Ohio soybean agricultural systems.Mycorrhiza · 2026Article
- Exploring Cervical Cancer-Associated Vaginal and Cervical Microbiota via 16S rRNA Sequencing.MicrobiologyOpen · 2026Article
- Environmental Sources and Tissue-Specific Selection Jointly Shape the Bacterial Community of the Sea Cucumber (Microorganisms · 2026Article
- Microbial transmission and ecology of human and environmental microbial communities in childcare centers.Research square · 2026Article
- Variation in Bird Gut Microbiota Across Dietary Guilds and Migratory Strategies.Ecology and evolution · 2026Article
- Rhizosphere Bacterial Communities of Two Coastal Halophytes Under Salinity-Flooding Stress.Plants (Basel, Switzerland) · 2026Article
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- Regulatory Effects of Tannin Supplementation on Microbial Succession and Flavor Formation During Xiaoqu Light-Flavor Baijiu Fermentation.Foods (Basel, Switzerland) · 2026Article
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- Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding.Microbiology spectrum · 2026Article
- Targeted amplicon sequencing for enhanced detection of spiked Shiga toxin-producingMicrobiology spectrum · 2026Article
- The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.Dermatology and therapy · 2026Review
- Comparative microbiome profiling of plant- and animal-derived traditional fermented foods from Mizoram, India using full-length 16S rRNA sequencing.Antonie van Leeuwenhoek · 2026Article
- Article
285 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important. Here we present a high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate. In two artificial communities of known composition, our method recovered the full complement of full-length 16S sequence variants from expected community members without residual errors. The measured abundances of intra-genomic sequence variants were in the integral ratios expected from the genuine allelic variants within a genome. The full-length 16S gene sequences recovered by our approach allowed Escherichia coli strains to be correctly classified to the O157:H7 and K12 sub-species clades. In human fecal samples, our method showed strong technical replication and was able to recover the full complement of 16S rRNA alleles in several E. coli strains. There are likely many applications beyond microbial profiling for which high-throughput amplicon sequencing of complete genes with single-nucleotide resolution will be of use.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.