Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, Peace Sandy

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
NSCLC
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Newly diagnosed NSCLC (non-small cell lung cancer) patients
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
39
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V2
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
4
Matched on Factors on which subjects have been matched on in a case-control study
age, body mass index, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 3 (B)

Description: (b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group

Abundance in Group 1: increased abundance in NSCLC

NCBI Quality ControlLinks
Pseudomonadota
Betaproteobacteria
Burkholderiales
Bacilli
Streptococcaceae
Streptococcus
Lactobacillales
Burkholderiaceae
Lautropia

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 3 (B)

Description: (b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group

Abundance in Group 1: decreased abundance in NSCLC

NCBI Quality ControlLinks
Porphyromonadaceae
Prevotella
Prevotella melaninogenica
Prevotellaceae
Bacteroidota
Bacteroidia
Bacteroidales

Revision editor(s): WikiWorks, Peace Sandy