ArticleScientific reports2023
16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Pooled it
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- Age, strain, and gut section shape the microbiome of commercial laying hens.Poultry science · 2026Article
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- Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.Microorganisms · 2026Review
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- Comparative analysis of MinION and MiSeq using 16S rRNA gene amplicon sequencing in human gut microbiome.BMC biotechnology · 2026Article
- Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.Frontiers in microbiology · 2026Article
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Genomics of host-microbiome interactions in humans.Nature reviews. Genetics · 2026Review
- Disentangling Gut Bacterial Community Patterns inInsects · 2025Article
- Analyzing human gut microbiome data from global populations: challenges and resources.Trends in microbiology · 2025Review
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Microbial Dysbiosis in the Lung and Gut in Response to Inhalable Particulate Matters in Pneumoconiosis Patients and Animals.Environmental science & technology · 2025Article
- Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer's disease?Current opinion in psychiatry · 2025Review
- Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.Journal of microbiology and biotechnology · 2025Review
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Article
- Human DNA hijacking microbiota surveys: causes and consequences in colon related 16s rRNA amplicon sequencing.Gut microbiome (Cambridge, England) · 2025Article
- Comparative analysis of full-length 16s ribosomal RNA gene sequencing in human oropharyngeal swabs using primer sets with different degrees of degeneracy.Frontiers in cellular and infection microbiology · 2025Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1-V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1-V2M primers. Moreover, the V1-V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1-V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.
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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.