Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
Head and neck carcinoma carcinoma of craniocervical region,carcinoma of head and neck,carcinoma of neck,carcinoma of the head and neck,carcinoma of the neck,craniocervical region carcinoma,head and neck cancer,head and neck carcinoma,neck carcinoma,Head and neck carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vocal cord polyp
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
32
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
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: increased abundance in Cancer

NCBI Quality ControlLinks
Enterobacter
Aggregatibacter
Pseudomonas
Azotobacter group

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: decreased abundance in Cancer

NCBI Quality ControlLinks
Fusobacterium
Prevotella
Filifactor
Actinobacillus
Helicobacter
Rikenellaceae
Eubacterium
Roseburia
Anaerovorax
Desulfovibrio
Johnsonella
Fusobacteriia
Fusobacteriota
Fusobacteriales
Fusobacteriaceae
Leptotrichiaceae
Peptostreptococcaceae
Candidatus Saccharibacteria
Sphingobacteriales
Sphingobacteriia
Lentimicrobiaceae
Helicobacteraceae
Candidatus Gracilibacteria
Caulobacteraceae
Caulobacterales
Defluviitaleaceae
Desulfovibrionaceae
Desulfovibrionales

Revision editor(s): WikiWorks