ArticleGenes2020
Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method.
Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it, 22 citations in OpenAlex.
- The Relationship Between Gut Microbiota, Muscle Mass and Physical Function in Older Individuals: A Systematic Review.Nutrients · 2024Pooled it
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods and a Vagina-Specific 16S rRNA Gene Database.Microorganisms · 2026Article
- Capturing clinically relevantMicrobial genomics · 2024Article
- Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis.Clinical and translational gastroenterology · 2024Article
- Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.Journal of virological methods · 2023Article
- Longitudinal comparison of the developing gut virome in infants and their mothers.Cell host & microbe · 2023Article
- Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach.Viruses · 2023Review
- Detection ofFrontiers in microbiology · 2023Article
- Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations.Scientific reports · 2021Article
- Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing.Frontiers in molecular biosciences · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Registered trials
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