ArticleBMC microbiology2014
Processing faecal samples: a step forward for standards in microbial community analysis.
Article in BMC microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
106 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren's Syndrome in a Systematic Review.Frontiers in immunology · 2021Pooled it
- Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota.The ISME journal · 2018Trial
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Multi-strain Bacillus Probiotics has Advantages in Improving Abnormal Behavior and Intestinal Flora in Rats of Autism Spectrum Disorder.Current microbiology · 2026Article
- Purification and Transcriptomic Characterization of Hypertrophied Hepatic Stellate Cells From CDAHFD Mouse Liver.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems.Environmental microbiome · 2025Article
- Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.Microorganisms · 2025Article
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Associations between the gut microbiota at one-year and neurodevelopment in children from the SEPAGES cohort.Brain, behavior, & immunity - health · 2025Article
- Faecal amino acids stability: investigating optimal sampling conditions for analysis.Metabolomics : Official journal of the Metabolomic Society · 2025Article
- Characterisation of the Faecal Microbiome of Alpacas Raised in South Eastern Australia.Animals : an open access journal from MDPI · 2025Article
- Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.Osong public health and research perspectives · 2025Article
- Article
- Stabilized and unstabilized sampling methods result in differential fecal 16S rRNA microbial sequencing results.PloS one · 2025Article
- Molecular Characterization Reveals Recombination and Host Exchange of Adenoviruses in Migratory Birds in China.Transboundary and emerging diseases · 2025Article
- Healthy human gut microbiome: Towards standardized research.AIMS microbiology · 2025Review
- Effect of fiber-modified kombucha tea on gut microbiota in healthy population: A randomized controlled trial (RCT).Current research in food science · 2025Article
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- A Comparison of Three Automated Nucleic Acid Extraction Systems for Human Stool Samples.Microorganisms · 2024Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe microbial community analysis of stools requires optimised and standardised protocols for their collection, homogenisation, microbial disruption and nucleic acid extraction. Here we examined whether different layers of the stool are equally representative of the microbiome. We also studied the effect of stool water content, which typically increases in diarrhoeic samples, and of a microbial disruption method on DNA integrity and, therefore, on providing an unbiased microbial composition analysis.
resultsWe collected faecal samples from healthy subjects and performed microbial composition analysis by pyrosequencing the V4 region of the 16S rRNA gene. To examine the effect of stool structure, we compared the inner and outer layers of the samples (N = 8). Both layers presented minor differences in microbial composition and abundance at the species level. These differences did not significantly bias the microbial community specific to an individual. To evaluate the effect of stool water content and bead-beating, we used various volumes of a water-based salt solution and beads of distinct weights before nucleic acid extraction (N = 4). The different proportions of water did not affect the UniFrac-based clustering of samples from the same subject However, the use or omission of a bead-beating step produced different proportions of Gram-positive and Gram-negative bacteria and significant changes in the UniFrac-based clustering of the samples.
conclusionThe degree of hydration and homogenisation of faecal samples do not significantly alter their microbial community composition. However, the use of bead-beating is critical for the proper detection of Gram-positive bacteria such as Blautia and Bifidobacterium.
Indexed as
Identifiers
What OpenQuestion holds
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.