ArticlemSphere2020
Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing.
Article in mSphere, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 3 of them syntheses 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
31 citing papers in PubMed, 3 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
- Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis.Microbiology spectrum · 2023Pooled it
- The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review.Gut microbes · 2020Pooled it
- Microbiome signatures for detection of colorectal lesions in population-based FIT screening.Nature communications · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.Microbiology spectrum · 2026Article
- Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.Cancer research communications · 2026Article
- Article
- Comparing the Metagenomic Performance of Stools Collected from Custom Cards and 95% Ethanol in Epidemiologic Studies.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025Article
- Field expedient stool collection methods for gut microbiome analysis in deployed military environments.mSphere · 2025Article
- Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.Genome medicine · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Review
- Nanopore R10.4 metagenomic detection of blaNature communications · 2024Article
- Associations between gut microbiota and incident fractures in the FINRISK cohort.NPJ biofilms and microbiomes · 2024Article
- Optimised human stool sample collection for multi-omic microbiota analysis.Scientific reports · 2024Article
- Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022].Nutrients · 2023Article
- A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies.Heliyon · 2023Article
- Assessing and removing the effect of unwanted technical variations in microbiome data.Scientific reports · 2022Article
- Vitamin B12 Status and Gut Microbiota among Saudi Females with Obesity.Foods (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.
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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.