Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients
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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
- China
- 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
- Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Probio group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the Probio group were instructed to take probiotic tablets orally
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 Weeks
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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: increased abundance in Probio group
Revision editor(s): Yjung24, Atrayees, Peace Sandy
Signature 2
Source: Figure 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: decreased abundance in Probio group
Revision editor(s): Yjung24, Peace Sandy
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CRC [colorectal cancer] Patients Pre-treatment group
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Fig 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: increased abundance in Probio group
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: decreased abundance in Probio group
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CRC [colorectal cancer] Patients Pre-treatment group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Placebo group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the Placebo group routinely treated with placebo tablets instead of probiotics
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: increased abundance in Placebo group
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Source: Fig 4
Description: LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.
Abundance in Group 1: decreased abundance in Placebo group
Revision editor(s): Peace Sandy
