The tongue microbiome in healthy subjects and patients with intra-oral halitosis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Claregrieve1, Davvve, Victoria
Subjects
- Location of subjects
- Netherlands
- 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
- Superior surface of tongue Dorsal surface of tongue,Superior surface of tongue,superior surface of tongue
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Halitosis oral halitosis,Halitosis,halitosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral Halitosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4
Description: Significant differentially abundant OTU of intr-aoral halitosis and Control
Abundance in Group 1: increased abundance in Oral Halitosis
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4
Description: Significant differentially abundant OTU of intra-oral halitosis and Control
Abundance in Group 1: decreased abundance in Oral Halitosis
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Haemophilus | ||
| Haemophilus parainfluenzae | ||
| Moryella | ||
| Oribacterium | ||
| Prevotella | ||
| Rothia dentocariosa | ||
| Streptococcus | ||
| Peptococcus | ||
| Leptotrichia |
