Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer
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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: 2022/09/29
Curator: Mary Bearkland
Revision editor(s): WikiWorks, LGeistlinger, Mary Bearkland, Peace Sandy
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
- Intestinal mucosa Bowel mucosa,Bowel mucosa of organ,Bowel mucous membrane,Bowel organ mucosa,Intestine mucosa,Intestine mucosa of organ,Intestine mucous membrane,Intestine organ mucosa,Mucosa of bowel,Mucosa of intestine,Mucosa of organ of bowel,Mucosa of organ of intestine,Mucous membrane of bowel,Mucous membrane of intestine,Organ mucosa of bowel,Organ mucosa of intestine,Tunica mucosa intestini,Intestinal mucosa,intestinal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Nutraceutical Dietary Supplement,Food Supplementation,Nutritional supplement,Nutraceutical,nutraceutical
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CGT group - colorectal cancer patients perioperative placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PGT group - colorectal cancer patients perioperative probiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Received antibiotics for the past 3 months prior to surgery
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- 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
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Curated date: 2022/09/29
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: increased abundance in PGT group - colorectal cancer patients perioperative probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Rhizobiaceae | ||
| Hyphomicrobiales | ||
| Rhizobium | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Alphaproteobacteria | ||
| Prevotellaceae |
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Signature 2
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: decreased abundance in PGT group - colorectal cancer patients perioperative probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Gemella | ||
| Bacillales Family X. Incertae Sedis | ||
| Peptostreptococcus | ||
| Anaerosporobacter |
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Experiment 2
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): WikiWorks, LGeistlinger, Mary Bearkland, Peace Sandy
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HGT Group - Healthy controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PGT group - colorectal cancer patients that received perioperative probiotics
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: increased abundance in PGT group - colorectal cancer patients perioperative probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Rhizobium | ||
| Rhizobiaceae | ||
| Hyphomicrobiales | ||
| Rhizobium sp. | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Alphaproteobacteria | ||
| Prevotellaceae |
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Signature 2
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: decreased abundance in PGT group - colorectal cancer patients perioperative probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Gemella | ||
| Bacillales Family X. Incertae Sedis | ||
| Peptostreptococcus | ||
| Anaerosporobacter |
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Experiment 3
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): WikiWorks, LGeistlinger, Mary Bearkland, Peace Sandy
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HGT- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CGT- colorectal cancer patients that received perioperative placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients that received perioperative placebos
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: increased abundance in CGT- colorectal cancer patients that received perioperative placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Gemella | ||
| Bacillales Family X. Incertae Sedis | ||
| Peptostreptococcus | ||
| Anaerosporobacter |
Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks
Signature 2
Curated date: 2022/09/30
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Mary Bearkland, Aiyshaaaa, Peace Sandy
Source: Fig 4
Description: Figure 4. Different structures of the gut microbiota in the CGT, PGT, and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.
Abundance in Group 1: decreased abundance in CGT- colorectal cancer patients that received perioperative placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadales | ||
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Pseudomonas | ||
| Pseudomonadaceae | ||
| Flavobacteriales | ||
| Flavobacteriaceae | ||
| Moraxellaceae |
Revision editor(s): WikiWorks, Mary Bearkland, Aiyshaaaa, Peace Sandy
