ArticleThe ISME journal2015
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.
Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed.
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- gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.Molecular ecology resources · 2025Article
- Macroecological patterns in experimental microbial communities.PLoS computational biology · 2025Article
- The oral-gut microbiome axis in health and disease.Nature reviews. Microbiology · 2024Review
- Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.Microbial ecology · 2024Article
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies.PloS one · 2024Article
- Bacterial bioindicators enable biological status classification along the continental Danube river.Communications biology · 2023Article
- Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs.eLife · 2023Article
- Purified Plant-Derived Phenolic Acids InhibitMicroorganisms · 2023Article
- Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections.Clinical oral investigations · 2023Article
- Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols.Food technology and biotechnology · 2023Article
- Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis.mSystems · 2023Article
- Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt.Environmental microbiology · 2023Article
- Association between Sleeping Patterns and Mealtime with Gut Microbiome: A Pilot Study.Archives of Iranian medicine · 2022Article
- Unsupervised Bayesian Ising Approximation for decoding neural activity and other biological dictionaries.eLife · 2022Article
- The early life microbiota mediates maternal effects on offspring growth in a nonhuman primate.iScience · 2022Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as one nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.
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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 OpenQuestion graph.