Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing/Experiment 2

From BugSigDB


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

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