Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study/Experiment 1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Rimsha, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Sweden
- 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
- Buccal mucosa , Lower lip Buccal mucosa,buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip,lower lip
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral mucositis inflammation of the mouth,oral cavity mucosal damage,oral mucosa irritation,oral mucosal damage,oral mucosal injury,oral mucosal lesions,stomatitis,Oral mucositis,oral mucositis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- reference
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with newly diagnosed malignancies
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- T-Test
- 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
- 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
Signature 1
Source: Figure 1a, Supplemental Table S2
Description: Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy)
Abundance in Group 1: increased abundance in patients with newly diagnosed malignancies
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Lactococcus | ||
| Derxia |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1a, Supplemental Table S2
Description: Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy)
Abundance in Group 1: decreased abundance in patients with newly diagnosed malignancies
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Corynebacterium | ||
| Coriobacteriaceae | ||
| Paludibacter | ||
| Sphingobacteriia | ||
| Gemella | ||
| Lachnospiraceae | ||
| Fusobacterium | ||
| Shewanella | ||
| Halomonas | ||
| Actinobacillus |
Revision editor(s): WikiWorks
