Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing/Experiment 2
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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
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
- Dental plaque Bacterial plaque,Plaque,Dental plaque,dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Iron deficiency anemia Ferropenic,Iron deficiency anaemia,Iron-deficiency anaemia,Iron-deficiency anemia,Iron deficiency anemia,iron deficiency anemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- iron deficiency anemia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with iron deficiency anemia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Source: Figure 5b
Description: LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients
Abundance in Group 1: increased abundance in iron deficiency anemia
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Source: Figure 5b
Description: LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients
Abundance in Group 1: decreased abundance in iron deficiency anemia
Revision editor(s): WikiWorks
