Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Rimsha, Claregrieve1, 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
Experiment 2
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no oral mucositis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oral mucositis
- 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) that has later developed oral mucositis (graded by the World Health Organization)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Table 2
Description: Comparison of the oral bacterial community at the time of malignancy diagnosis (before chemotherapy) in patients who later developed oral mucositis and those who did not develop oral mucositis
Abundance in Group 1: increased abundance in oral mucositis
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga | ||
| Fusobacteriota | ||
| Lactococcus | ||
| Spirochaeta | ||
| Peptostreptococcaceae incertae sedis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- at malignancy diagnosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- during chemotherapy
- 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 that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: Table 3
Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis
Abundance in Group 1: increased abundance in during chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table 3
Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis
Abundance in Group 1: decreased abundance in during chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Derxia | ||
| Pseudomonadota |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Subjects
- 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 that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that did not develop oral mucositis (graded by the World Health Organization) during chemotherapy treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Table 3
Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who do not have oral mucositis
Abundance in Group 1: increased abundance in during chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Xanthomonas |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- all samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mucositis lesions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples from mucositis lesions
- Group 0 sample size Number of subjects in the control (unexposed) group
- 97
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Signature 1
Source: Supplemental Table S4, Figure S1, S2
Description: Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions
Abundance in Group 1: increased abundance in mucositis lesions
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Supplemental Table S4, Figure S1, S2
Description: Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions
Abundance in Group 1: decreased abundance in mucositis lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Aggregatibacter | ||
| Haemophilus |
Revision editor(s): Claregrieve1, WikiWorks
