ArticlemSphere2021
Comparison of Fecal Collection Methods on Variation in Gut Metagenomics and Untargeted Metabolomics.
Article in mSphere, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fecal microbiota transplantation treatment of autoimmune-mediated type 1 diabetes: A systematic review.Frontiers in cellular and infection microbiology · 2022Pooled it
- The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.Environmental health perspectives · 2026Article
- Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.Scientific reports · 2026Article
- S'Wipe: user-friendly stool collection for high-throughput gut metabolomics and multi-omics.mSystems · 2026Article
- Effects of repeated freeze and thaw cycles on the stability of faecal microbiome composition.Scientific reports · 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
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- OMNImet®•GUT collection kit supports sample collection and ambient temperature preservation of faecal short chain fatty acids.Metabolomics : Official journal of the Metabolomic Society · 2025Article
- Fecal microbiomes from screening sampling tubes are stable despite varying sampling and storage conditions.Scientific reports · 2025Article
- Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.Nature microbiology · 2025Article
- Field expedient stool collection methods for gut microbiome analysis in deployed military environments.mSphere · 2025Article
- HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.Biology · 2025Article
- Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.Microorganisms · 2025Article
- Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism.NPJ biofilms and microbiomes · 2025Article
- Standardization of Fecal Metabolomics Using Microbiome Preservation Kits: Implications for Multiomics Integration.International journal of analytical chemistry · 2025Article
- Omnigene-GutAMB Express · 2024Article
- Article
- Endoscopic brush sampling identifies mucosa associated microbiota in colorectal adenomas.Heliyon · 2024Article
- Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review).Experimental and therapeutic medicine · 2024Review
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at -80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies.
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