ArticleProceedings of the National Academy of Sciences of the United States of America2015
Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
115 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.Microbiology spectrum · 2022Pooled it
- Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review.Frontiers in public health · 2019Pooled it
- Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva.Investigative ophthalmology & visual science · 2016Trial
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Optimized protocol for profiling mucosa-associated microbiota from formalin-fixed paraffin-embedded gut tissues from treatment-naïve pediatric patients with Crohn's disease.Frontiers in cellular and infection microbiology · 2026Article
- Absolute Quantification of Bacteria in the Microbiome and Its Application.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems.Environmental microbiome · 2025Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.Environmental microbiology reports · 2025Article
- Genomic GC bias correction improves species abundance estimation from metagenomic data.Nature communications · 2025Article
- Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.Molecular ecology resources · 2025Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Exploring the cecal microbial community associated with fat deposition in sheep and its possible pathways of action.Microbiology spectrum · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- Cross-comparison of gut metagenomic profiling strategies.Communications biology · 2024Article
- Article
- Standardization of gut microbiome analysis in sports.Cell reports. Medicine · 2024Review
- Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples.Archives of microbiology · 2024Article
- A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria.International microbiology : the official journal of the Spanish Society for Microbiology · 2024Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.
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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.