ArticleNature methods2022
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
217 citing papers in PubMed, 361 citations in OpenAlex.
- Effects of Uro-Vaxom vs. placebo on the urinary tract microbiome in individuals with spinal cord injury in a randomized controlled pilot trial (Uro-Vaxom pilot).Scientific reports · 2025Trial
- An NGS-assisted diagnostic workflow for culture-independent detection of bloodstream pathogens and prediction of antimicrobial resistances in sepsis.Frontiers in cellular and infection microbiology · 2025Trial
- Full-length 16S rRNA nanopore sequencing enables species resolution ofGut microbes · 2026Article
- Microbiota shows major difference in case of two shorebird species with different feeding strategy.Veterinary and animal science · 2026Article
- Expanded proinflammatory CD4 T cells expressing toll like receptor 4 in trauma associated acute lung injury.Communications biology · 2026Article
- Life stage shifts in salivary microbiota determinants: a cross-sectional study in twins.NPJ biofilms and microbiomes · 2026Article
- Machine learning identifies key microbial signatures for Salmonella enteritidis colonization and persistence in broiler ceca.Poultry science · 2026Article
- A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.Microbial genomics · 2026Article
- Gut microbiome alterations are sex-dependently associated with brain abnormalities in a mouse model of Neurofibromatosis type I.Molecular psychiatry · 2026Article
- Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.Journal of fish diseases · 2026Article
- Anaerobic metabolic responses of sludge and mine wastewater-derived consortia to winery wastewater-related compounds.World journal of microbiology & biotechnology · 2026Article
- Performance and practicality of 16S nanopore sequencing for routine bacterial identification in clinical samples.Microbiology spectrum · 2026Article
- Age- and sex-related differences in early-life gut microbiota and intestinal physiology in broiler chickens.Journal of animal science and biotechnology · 2026Article
- Article
- Effects of Dietary Supplementation withBiology · 2026Article
- Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.BMC microbiology · 2026Article
- Pharmacokinetics of Long-Acting Ampicillin and Its Impact on the Gut Microbiome and Resistome in Rhesus Macaques (Macaca mulatta).Journal of veterinary pharmacology and therapeutics · 2026Article
- The Establishment of an Indigenous-Led Drinking Water Monitoring Program Leveraging qPCR and Metagenomics Testing in New Zealand.Water environment research : a research publication of the Water Environment Federation · 2026Article
- The root exudates of wild tomato compared to a modern variety maintain elevated soluble soil phosphorus by interacting with rhizosphere microbiota.Scientific reports · 2026Article
- Canine Fecal Microbiome Dataset: Ultra-deep Multi-platform Sequencing Across Extraction and Library Protocols.Scientific data · 2026Article
157 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 5 institutions in 2 countries.
Funding
Abstract
16S ribosomal RNA-based analysis is the established standard for elucidating the composition of microbial communities. While short-read 16S rRNA analyses are largely confined to genus-level resolution at best, given that only a portion of the gene is sequenced, full-length 16S rRNA gene amplicon sequences have the potential to provide species-level accuracy. However, existing taxonomic identification algorithms are not optimized for the increased read length and error rate often observed in long-read data. Here we present Emu, an approach that uses an expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. Results produced from simulated datasets and mock communities show that Emu is capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative methods. Additionally, we illustrate a real-world application of Emu by comparing clinical sample composition estimates generated by an established whole-genome shotgun sequencing workflow with those returned by full-length 16S rRNA gene sequences processed with Emu.
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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 OpenQuestion graph.