Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R, Vogtmann E
Journal
BMC microbiology
Year
2021
Keywords:
Comparability, Feces, Iran, Microbiome, Saliva, Stability
BACKGROUND: To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. RESULTS: We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. CONCLUSIONS: As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.
Experiment 1
Subjects
- Location of subjects
- Iran
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Fecal Occult Blood Test (FOBT card)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- RNAlater
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- fecal sample collected with RNAlater stabilizing solution.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 136
- Group 1 sample size Number of subjects in the case (exposed) group
- 133
Lab analysis
- Sequencing type
- PCR
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Additional files 2 Table S4
Description: Differential abundance analysis of phylum level changes comparing RNAlater to FOBT card fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran
Abundance in Group 1: increased abundance in RNAlater
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Cyanobacteriota | ||
| Lentisphaerota | ||
| Mycoplasmatota | ||
| Pseudomonadota | ||
| Verrucomicrobiota |
Revision editor(s): EGO
Signature 2
Source: Additional files 2 Table S4
Description: Differential abundance analysis of phylum level changes comparing RNAlater to FOBT card fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran
Abundance in Group 1: decreased abundance in RNAlater
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota |
Revision editor(s): EGO
Experiment 2
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- OMNIgene ORAL kits
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Scope mouthwash
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oral sample collected with Scope mouthwash
- Group 0 sample size Number of subjects in the control (unexposed) group
- 77
- Group 1 sample size Number of subjects in the case (exposed) group
- 125
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Additional files 2 Table S8
Description: Differential abundance analysis of phylum level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran
Abundance in Group 1: increased abundance in Scope mouthwash
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Campylobacterota | ||
| Patescibacteria group | ||
| Spirochaetota |
Revision editor(s): EGO
Signature 2
Source: Additional files 2 Table S8
Description: Differential abundance analysis of phylum level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran
Abundance in Group 1: decreased abundance in Scope mouthwash
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): EGO
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