16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-26
Subjects
- Location of subjects
- France
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Non-Hodgkins lymphoma NHL,non-Hodgkin lymphoma,non-Hodgkin's lymphoma,non-Hodgkin's lymphoma (NHL),non-Hodgkins lymphoma,Non-Hodgkins lymphoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-chemotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-chemotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- all antibiotics after starting chemotherapy
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- 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
- Mann-Whitney (Wilcoxon)
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-26
Source: Figure 4, 5, text
Description: Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data
Abundance in Group 1: increased abundance in post-chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroidota | ||
| Escherichia | ||
| Pseudomonadota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-26
Source: Figure 4, 5, text
Description: Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data
Abundance in Group 1: decreased abundance in post-chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Actinomycetota | ||
| Blautia | ||
| Faecalibacterium | ||
| Roseburia | ||
| Bifidobacterium |
