ArticleFrontiers in microbiology2021
Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
- Lawsonia intracellularis infection induces changes in microbial community function and composition associated with reduced pig growth and feed efficiency.Animal microbiome · 2026Article
- Leveraging real-time genomic surveillance to combat infectious diseases and antimicrobial resistance in cancer patients.Frontiers in public health · 2026Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Lacticaseibacillus paracasei Glu-07: A Promising Probiotic Candidate for the Management of Type 2 Diabetes Mellitus.Current microbiology · 2025Article
- Unveiling the impact of 16S rRNA gene intergenomic variation on primer design and gut microbiome profiling.Frontiers in microbiology · 2025Article
- Position statement of the Microbiota International Clinical Society.Frontiers in microbiomes · 2025Article
- Article
- The Characteristics of Gut Microbiota and Its Relation with Diet in Postmenopausal Osteoporosis.Calcified tissue international · 2024Article
- Associations between gut microbiota and incident fractures in the FINRISK cohort.NPJ biofilms and microbiomes · 2024Article
- Phage-inclusive profiling of human gut microbiomes with Phanta.Nature biotechnology · 2024Article
- Data-driven prediction of colonization outcomes for complex microbial communities.Nature communications · 2024Article
- On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.Microbial genomics · 2024Article
- Gut microbiota changes associated with low-carbohydrate diet intervention for obesity.Open life sciences · 2024Article
- Lactobacillus oris improves non-alcoholic fatty liver in mice and inhibits endogenous cholesterol biosynthesis.Scientific reports · 2023Article
- Identification of colorectal cancer progression-associated intestinal microbiome and predictive signature construction.Journal of translational medicine · 2023Article
- The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions.FEMS microbiology reviews · 2023Article
- Evolving understanding of rumen methanogen ecophysiology.Frontiers in microbiology · 2023Review
- Risk of bias assessment tool for systematic review and meta-analysis of the gut microbiome.Gut microbiome (Cambridge, England) · 2023Article
- Effect of Husbandry Practices on the Fecal Microbiota of C57BL/6J Breeding Colonies Housed in 2 Different Barrier Facilities in the Same Institution.Journal of the American Association for Laboratory Animal Science : JAALAS · 2023Article
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.
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