Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 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
- Mann-Whitney (Wilcoxon)
- 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
- 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
Source: Figure 3b, 4b, Table S2
Description: Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients
Abundance in Group 1: increased abundance in iron deficiency anemia
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Moraxella | ||
Lactococcus | ||
Pseudomonas | ||
Enterococcus | ||
Kocuria | ||
Lactobacillus |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3b, 4b, Table S2
Description: Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients
Abundance in Group 1: decreased abundance in iron deficiency anemia
NCBI | Quality Control | Links |
---|---|---|
Actinomycetota | ||
Corynebacterium | ||
Neisseria | ||
Aggregatibacter | ||
Cardiobacterium |
Revision editor(s): WikiWorks
Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
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
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
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
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- iron deficiency anemia moderate
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- iron deficiency anemia severe
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- iron defiency anemia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5d
Description: LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients
Abundance in Group 1: increased abundance in iron deficiency anemia severe
Revision editor(s): WikiWorks
Signature 2
Source: Figure 5d
Description: LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients
Abundance in Group 1: decreased abundance in iron deficiency anemia severe
NCBI | Quality Control | Links |
---|---|---|
Pasteurellales | ||
Pasteurellaceae | ||
Neisseriales | ||
Neisseriaceae |
Revision editor(s): WikiWorks