Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients
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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
Subjects
- Location of subjects
- Netherlands
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no ulcerative oral mucositis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ulcerative oral mucositis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient developed uclerative oral mucositis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
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
- RT-qPCR
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
- 2
Signature 1
Source: Figure 3
Description: Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe
Abundance in Group 1: increased abundance in ulcerative oral mucositis
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Enterococcus | ||
| Streptococcus | ||
| Staphylococcus | ||
| Fusobacterium | ||
| Prevotella |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3
Description: Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe
Abundance in Group 1: decreased abundance in ulcerative oral mucositis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Actinomyces |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- one and two weeks after stem cell transplant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre- and three month after auto stem cell transplant
Lab analysis
Statistical Analysis
- Statistical test
- PERMANOVA
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: text
Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group
Abundance in Group 1: increased abundance in pre- and three month after auto stem cell transplant
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella atypica | ||
| Veillonella dispar | ||
| Actinomyces sp. | ||
| Actinomyces graevenitzii | ||
| Prevotella | ||
| Leptotrichia | ||
| Megasphaera micronuciformis | ||
| Veillonella sp. |
Signature 2
Source: text
Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group
Abundance in Group 1: decreased abundance in pre- and three month after auto stem cell transplant
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Limosilactobacillus fermentum | ||
| Scardovia wiggsiae |
Experiment 3
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: text
Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group
Abundance in Group 1: increased abundance in pre- and three month after auto stem cell transplant
Signature 2
Source: text
Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group
Abundance in Group 1: decreased abundance in pre- and three month after auto stem cell transplant
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus | ||
| Staphylococcus caprae | ||
| Staphylococcus epidermidis | ||
| Staphylococcus warneri | ||
| Scardovia wiggsiae | ||
| Enterococcus faecalis |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low or no fungi load
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 0.1% or higher fungi load
Signature 1
Source: text
Description: Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA
Abundance in Group 1: increased abundance in 0.1% or higher fungi load
| NCBI | Quality Control | Links |
|---|---|---|
| Scardovia | ||
| Staphylococcus | ||
| Lactobacillus |
Signature 2
Source: text
Description: Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA
Abundance in Group 1: decreased abundance in 0.1% or higher fungi load
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Actinomyces | ||
| Prevotella | ||
| Leptotrichia | ||
| Megasphaera | ||
| Streptococcus |
