ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2023
Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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.
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Who cites it
16 citing papers in PubMed.
- Separating extracellular from intracellular fecal metabolites exposes cross-feeding architecture in the gut: exploring metabolite partitioning and ecological associations.Gut microbes · 2026Article
- Behavioural phase transitions in the migratory locust,ISME communications · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- Genomic GC bias correction improves species abundance estimation from metagenomic data.Nature communications · 2025Article
- Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.bioRxiv : the preprint server for biology · 2025Article
- Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.Microorganisms · 2025Article
- Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.Frontiers in microbiomes · 2025Article
- Advanced Membrane Simulations in Probiotics and Gut Microbiome Interaction Research: The Current Trends and Insights.Current pharmaceutical design · 2025Review
- A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.Microbes and environments · 2025Article
- Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis.PloS one · 2025Article
- Interplay between host genetics and gut microbiome composition in the Japanese population.Frontiers in microbiomes · 2025Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.Communications biology · 2024Article
- Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Animals : an open access journal from MDPI · 2024Article
- Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies.Applied microbiology and biotechnology · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.
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Registered trials
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