Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts/Experiment 1
From BugSigDB
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
