ArticleMicrobiology spectrum2022
Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Draft genome sequences of four strains ofMicrobiology resource announcements · 2026Article
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- Simple endpoint PCR assay using portable devices for Escherichia coli quantification in water samples.Environmental monitoring and assessment · 2026Article
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Setting higher standards for reports of microbial species in human cancers.Nature cancer · 2026Review
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- Article
- De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.Microbiome · 2025Article
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.Nature communications · 2025Article
- The human microbiome in clinical translation: from bench to bedside.Frontiers in microbiology · 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
- State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.Frontiers in reproductive health · 2025Review
- Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.Communications biology · 2024Article
- Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.Scientific data · 2024Article
- Benchmarking DNA isolation methods for marine metagenomics.Scientific reports · 2023Article
- Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment.Emerging infectious diseases · 2023Article
- Article
- Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control.
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