Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing

From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-7
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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Bacillota
Moraxella
Lactococcus
Pseudomonas
Enterococcus
Kocuria
Lactobacillus

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-17

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

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

NCBI Quality ControlLinks
Bacilli
Enterococcaceae
Enterococcus
Bacillota
Kocuria
Lactobacillales
Lactococcus
Moraxella
Moraxellaceae
Peptostreptococcaceae
Pseudomonadales
Pseudomonas
Streptococcaceae
Pseudomonadaceae

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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

NCBI Quality ControlLinks
Campylobacterota
Campylobacterales
Campylobacteraceae
Campylobacter
Cardiobacteriaceae
Cardiobacteriales
Cardiobacterium
Rothia
Aggregatibacter
Caldimonas
Burkholderiales
Capnocytophaga
Flavobacteriia
Flavobacteriaceae
Flavobacteriales
Pasteurellaceae
Pasteurellales
Neisseria
Neisseriaceae
Neisseriales
Betaproteobacteria
Mycobacteriales
Corynebacteriaceae
Corynebacterium
Actinomycetota
Actinomycetes

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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

NCBI Quality ControlLinks
Kocuria
Porphyrobacter
Bifidobacteriaceae
Staphylococcus
Staphylococcaceae
Moraxella
Moraxellaceae
Enterococcus
Enterococcaceae
Pseudomonas
Azotobacter group
Bacillota
Gammaproteobacteria
Lactococcus
Pseudomonadales

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Pasteurellales
Pasteurellaceae
Neisseriales
Neisseriaceae

Revision editor(s): WikiWorks