ArticleScientific data2020
Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample.
Article in Scientific data, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 4 of them syntheses that pooled it.
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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
43 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies.Alimentary pharmacology & therapeutics · 2025Pooled it
- Checkpoint inhibitor responses can be regulated by the gut microbiota - A systematic review.Neoplasia (New York, N.Y.) · 2023Pooled it
- The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.Heart failure reviews · 2022Pooled it
- Characterization of the Oral and Gut Microbiota in Patients with Psoriatic Diseases: A Systematic Review.Acta dermato-venereologica · 2021Pooled it
- Coenocline Simulation of Microbiome Samples: A Biologically Mechanistic Framework for Generating Ecologically Realistic Synthetic Datasets to Support Classification Method Evaluation.Pathogens (Basel, Switzerland) · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- The microbiome and its impact on the epigenome in cancer.Frontiers in epigenetics and epigenomics · 2026Review
- QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.Microbiology spectrum · 2025Article
- Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.Journal of the American Statistical Association · 2025Article
- Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.NPJ biofilms and microbiomes · 2025Article
- Nutritional Strategies in Major Depression Disorder: From Ketogenic Diet to Modulation of the Microbiota-Gut-Brain Axis.Molecular neurobiology · 2025Review
- Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.Polish journal of microbiology · 2025Article
- Tertiary lymphoid structures: exploring opportunities to improve immunotherapy in ovarian cancer.Frontiers in immunology · 2025Review
- A Narrative Review of the Putative Etiologic Role and Diagnostic Utility of the Cervicovaginal Microbiome in Human Papillomavirus-Associated Cervical Carcinogenesis.Journal of medical virology · 2024Review
- Article
- Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota.BMC genomics · 2024Article
- KL-Biome (Postbiotic Formulation ofInternational journal of molecular sciences · 2024Article
- Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota.Current genomics · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Multi-class boosting for the analysis of multiple incomplete views on microbiome data.BMC bioinformatics · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.
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Registered trials
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.