Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus/Experiment 1
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Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Curated date: 2024/05/02
Curator: Scholastica
Revision editor(s): WikiWorks, Scholastica, Aleru Divine, Ifeanyisam
Subjects
- Location of subjects
- China
- 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
- Oral cavity , Esophagus Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,Gullet,Oesophagus,Esophagus,esophagus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Health study participationHealth study participation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral cavity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Esophagus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 3, Supplementary Figure S1
Description: Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis
Abundance in Group 1: increased abundance in Esophagus
Revision editor(s): Scholastica, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 3, Supplementary Figure S1
Description: Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis
Abundance in Group 1: decreased abundance in Esophagus
Revision editor(s): Scholastica, WikiWorks
