ArticleJournal of visualized experiments : JoVE2014
Next-generation sequencing of 16S ribosomal RNA gene amplicons.
Article in Journal of visualized experiments : JoVE, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
84 citing papers in PubMed, 119 citations in OpenAlex.
- Safety assessment scheme for menstrual cups and application for the evaluation of a menstrual cup comprised of medical grade silicone.EBioMedicine · 2022Trial
- Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.Microorganisms · 2026Review
- Evaluation of Germplasm Resources and Microbial Diversity Among Different Geographical Provenances ofMicroorganisms · 2026Article
- Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients.Scientific reports · 2026Article
- Integrated analysis of gut microbiota structure and metabolic function in patients with cirrhosis and refractory ascites.Biomedical reports · 2026Article
- Gut microbiota profile and response to neoadjuvant chemoradiotherapy in patients with rectal cancer: a systematic review.Translational gastroenterology and hepatology · 2026Review
- Omics-enhanced nanomedicine: integrating multi-omics for precision cancer diagnosis and therapy.Discover oncology · 2025Review
- PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.Current issues in molecular biology · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- Metabolomics-based analysis of the correlation between lipid metabolites and thyroid carcinoma.BMC biotechnology · 2025Article
- Skin Microbiome Shifts in Various Dermatological Conditions.Journal of clinical medicine · 2025Review
- A Natural Language Processing Method Identifies an Association Between Bacterial Communities in the Upper Genital Tract and Ovarian Cancer.International journal of molecular sciences · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Article
- Cancer microbiota: a focus on tumor-resident bacteria.EMBO reports · 2025Review
- Susceptibility to Postbiotic Substances-Enterocins of the StrainsPathogens (Basel, Switzerland) · 2025Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Alpine radish rhizosphere microbiome assembly and metabolic adaptation under PBAT/PLA humic acid biodegradable mulch films.Frontiers in microbiology · 2025Article
- Halophilic rhizobacteria promote growth, physiology and salinity tolerance inFrontiers in microbiology · 2025Article
- Celiac disease and human gut microbiota - how can we study the composition of microorganisms?Przeglad gastroenterologiczny · 2025Review
24 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
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.
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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.