Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- United States of America
- 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
- Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Salivary Microbiome pre treatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Salivary Microbiome post treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Changes in the oral microbiome from pre- to post-treatment saliva collected from patients with SCC at diagnosis and 6 months later (0 and 6 months), to identify changes that occurred soon after completion of therapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 106
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 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
- 2.5
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 3
Needs review
Source: Figure 1F
Description: Significance of bacterial families that were at least 0.1% in differential abundance.
Abundance in Group 1: increased abundance in Salivary Microbiome post treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Burkholderiaceae | ||
| Lachnospiraceae | ||
| Lactobacillaceae | ||
| Prevotellaceae | ||
| Pseudomonadaceae | ||
| Staphylococcaceae | ||
| unclassified Lactobacillales | ||
| Leptotrichiaceae |
Revision editor(s): Nityasinghal 14
Signature 4
Needs review
Source: Figure 1F
Description: Significance of bacterial families that were at least 0.1% in differential abundance.
Abundance in Group 1: decreased abundance in Salivary Microbiome post treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichaceae | ||
| Flavobacteriaceae | ||
| Neisseriaceae | ||
| Pasteurellaceae | ||
| Peptostreptococcaceae | ||
| Porphyromonadaceae | ||
| unclassified Bacteroidales |
Revision editor(s): Nityasinghal 14
