Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing
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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.
URI
Authors
Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X, Li J
Journal
BMC oral health
Year
2019
Keywords:
High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota
BACKGROUND: The relationship between oral microbiota and IE (infective endocarditis) is well established. Opportunistic pathogens in normal oral flora enter the bloodstream through daily oral cleaning or invasive dental procedures, leading to the occurrence of infective endocarditis. An in vitro iron-deficient condition leads to a drastic community shift in oral microbiota with increasing proportions of taxa related to infective endocarditis. To investigate the relationship among insufficient iron supply, oral microbiota and the risk of IE and to conduct a population amplification study, iron-deficiency anaemia is used as an in vivo model. METHODS: This cross-sectional study enrolled 24 primary iron-deficiency anemia (IDA) patients from 2015.6 to 2016.6 from the hematology department of West China Hospital, Sichuan University, and 24 healthy controls. High-throughput sequencing compared the dental plaque microbiota of 24 IDA (iron-deficiency anaemia) patients and 24 healthy controls. RESULTS: Sequences were classified into 12 phyla, 28 classes, 50 orders, 161 genera and 497 OTUs (the IDA and control groups shared the same 384 OTUs). Iron deficiency leads to lower internal diversity in the oral flora. The abundances of genera Corynebacterium, Neisseria, Cardiobacterium, Capnocytophaga, and Aggregatibacter were significantly higher in healthy controls, while genera Lactococcus, Enterococcus, Lactobacillus, Pseudomonas and Moraxella showed higher proportions in the IDA group (P < 0.05). The relative abundances of genera Lactococcus, Enterococcus, Pseudomonas and Moraxella were significantly negatively correlated with the concentration of serum ferritin (P < 0.05). CONCLUSIONS: Without an increase of oral streptococci, the main pathogen of IE, it is difficult to determine whether IDA can increase the risk of IE. However, the iron-deficient condition did lead to changes in the oral microbiota community structure. The genera that showed higher proportions in the IDA group were frequently reported as antibiotic-resistant. As antibiotics are commonly recommended to prevent IE before dental procedures, this study offers new ideas of personalized prevention of IE.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-7
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-17
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
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
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
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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: decreased abundance in iron deficiency anemia severe
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurellales | ||
| Pasteurellaceae | ||
| Neisseriales | ||
| Neisseriaceae |
Revision editor(s): WikiWorks
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