ArticleApplied and environmental microbiology2014
Evaluating bias of illumina-based bacterial 16S rRNA gene profiles.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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Who cites it
126 citing papers in PubMed.
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- Microbiome interactions in renal cell carcinoma: evidence, challenges and opportunities.Nature reviews. Urology · 2026Review
- The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer.Oncogene · 2026Review
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.International journal of molecular sciences · 2025Article
- L-Arabinose Alleviates Functional Constipation in Mice by Regulating Gut Microbiota and Metabolites.Foods (Basel, Switzerland) · 2025Article
- Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.Applied and environmental microbiology · 2025Article
- Characteristics and Differences in the Antler Velvet Microbiota During Regeneration.Microorganisms · 2024Article
- A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.Science advances · 2024Article
- Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite.Environmental microbiology reports · 2024Article
- Changes in social environment impact primate gut microbiota composition.Animal microbiome · 2024Article
- The Ocular Microbiome: Micro-Steps Towards Macro-Shift in Targeted Treatment? A Comprehensive Review.Microorganisms · 2024Review
- Unveiling the hidden world: How arbuscular mycorrhizal fungi and its regulated core fungi modify the composition and metabolism of soybean rhizosphere microbiome.Environmental microbiome · 2024Article
- NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.Genome biology · 2024Article
- Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.Communications biology · 2024Article
- Harnessing the power of microbes: Enhancing soybean growth in an acidic soil through AMF inoculation rather than P-fertilization.Horticulture research · 2024Article
- Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.Scientific reports · 2024Article
- Article
- eDNA-Based Early Detection Illustrates Rapid Spread of the Non-Native Golden Mussel Introduced into Beijing via Water Diversion.Animals : an open access journal from MDPI · 2024Article
- Quantitative Aggregation of Microbiome Sequencing Data Provides Insights into the Associations between the Skin Microbiome and Psoriasis.JID innovations : skin science from molecules to population health · 2024Article
66 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Massively parallel sequencing of 16S rRNA genes enables the comparison of terrestrial, aquatic, and host-associated microbial communities with sufficient sequencing depth for robust assessments of both alpha and beta diversity. Establishing standardized protocols for the analysis of microbial communities is dependent on increasing the reproducibility of PCR-based molecular surveys by minimizing sources of methodological bias. In this study, we tested the effects of template concentration, pooling of PCR amplicons, and sample preparation/interlane sequencing on the reproducibility associated with paired-end Illumina sequencing of bacterial 16S rRNA genes. Using DNA extracts from soil and fecal samples as templates, we sequenced pooled amplicons and individual reactions for both high (5- to 10-ng) and low (0.1-ng) template concentrations. In addition, all experimental manipulations were repeated on two separate days and sequenced on two different Illumina MiSeq lanes. Although within-sample sequence profiles were highly consistent, template concentration had a significant impact on sample profile variability for most samples. Pooling of multiple PCR amplicons, sample preparation, and interlane variability did not influence sample sequence data significantly. This systematic analysis underlines the importance of optimizing template concentration in order to minimize variability in microbial-community surveys and indicates that the practice of pooling multiple PCR amplicons prior to sequencing contributes proportionally less to reducing bias in 16S rRNA gene surveys with next-generation sequencing.
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