Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer
-
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 (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients perioperative placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: increased abundance in colorectal cancer patients perioperative probiotics
Revision editor(s): Mary Bearkland
Signature 2
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: decreased abundance in colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Coprococcus | |
| Sphingomonas ⚠ | |
| Comamonas ⚠ | |
| Fusobacteriota |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Location of subjects
- China
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: increased abundance in colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Bacillota | |
| Bacillus ⚠ | |
| Carnobacterium | |
| Enterococcus | |
| Rhizobium ⚠ | |
| Escherichia/Shigella sp. | |
| Nevskia ⚠ | |
| Fusobacteriota | |
| Rhodococcus ⚠ |
Revision editor(s): Mary Bearkland
Signature 2
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: decreased abundance in colorectal cancer patients perioperative probiotics
Revision editor(s): Mary Bearkland
Experiment 3
Subjects
- Location of subjects
- China
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients perioperative placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the CGT group received encapsulated maltodextrin (Haiyan Liuhe Pharmaceutical Industry Co., Ltd., Jiangsu, China) three times a day. During the study period, no parenteral or enteral nutritional
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
Signature 1
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: increased abundance in colorectal cancer patients perioperative placebo
| NCBI | Links |
|---|---|
| Enterococcus | |
| Peptostreptococcus | |
| Fusobacteriota | |
| Fusobacterium |
Revision editor(s): Mary Bearkland
Signature 2
Source: Table 3
Description: Comparison of gut microflora structure at phylum and genus levels.
Abundance in Group 1: decreased abundance in colorectal cancer patients perioperative placebo
Revision editor(s): Mary Bearkland
Experiment 4
Subjects
- Location of subjects
- China
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients perioperative placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- LEfSe
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 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 colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Escherichia/Shigella sp. | |
| Rhizobiaceae | |
| Rhizobium ⚠ | |
| Hyphomicrobiales | |
| Enterococcaceae | |
| Enterococcus | |
| Alphaproteobacteria | |
| Prevotellaceae |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 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 colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Flavobacteriaceae | |
| Flavobacteriales | |
| Gammaproteobacteria | |
| Moraxellaceae | |
| Pseudomonadota | |
| Pseudomonadaceae | |
| Pseudomonadales | |
| Pseudomonas ⚠ | |
| Flavobacteriia |
Revision editor(s): Mary Bearkland
Experiment 5
Subjects
- Location of subjects
- China
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients perioperative placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 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 colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Escherichia/Shigella sp. | |
| Rhizobiaceae | |
| Rhizobium ⚠ | |
| Hyphomicrobiales | |
| Enterococcaceae | |
| Enterococcus | |
| Alphaproteobacteria | |
| Prevotellaceae |
Revision editor(s): Mary Bearkland
Signature 3
Source: Figure 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 colorectal cancer patients perioperative probiotics
| NCBI | Links |
|---|---|
| Fusobacteriaceae | |
| Fusobacterium | |
| Gemella | |
| Peptostreptococcus | |
| Anaerosporobacter | |
| Family_XI_incertae_sedisFamily_XI_incertae_sedis |
Revision editor(s): Mary Bearkland
Experiment 6
Subjects
- Location of subjects
- China
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- NutraceuticalsNutraceuticals
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients perioperative placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the CGT group received encapsulated maltodextrin (Haiyan Liuhe Pharmaceutical Industry Co., Ltd., Jiangsu, China) three times a day. During the study period, no parenteral or enteral nutritional
- 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)
- No antibiotics for 3 months preceding surgery
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
Signature 1
Source: Figure 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 colorectal cancer patients perioperative placebo
| NCBI | Links |
|---|---|
| Fusobacteriaceae | |
| Fusobacterium | |
| Gemella | |
| family XI incertae sedisfamily XI incertae sedis | |
| Peptostreptococcus | |
| Anaerosporobacter |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 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 colorectal cancer patients perioperative placebo
| NCBI | Links |
|---|---|
| Pseudomonadales | |
| Pseudomonadota | |
| Gammaproteobacteria | |
| Pseudomonas ⚠ | |
| Pseudomonadaceae | |
| Flavobacteriales | |
| Flavobacteriia | |
| Moraxellaceae | |
| Flavobacteriaceae |
Revision editor(s): Mary Bearkland
