Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative 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
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mary Bearkland, Peace Sandy, Joiejoie
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
- Nutraceutical , Colorectal carcinoma Dietary Supplement,Food Supplementation,Nutritional supplement,Nutraceutical,nutraceutical
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients who didn't take prebiotics (preoperative fecal sample)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients who took prebiotics (preoperative fecal sample)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with radiologic and pathologic diagnosis of CRC (preoperatively). Patients in the intervention group (prebiotic group) received a daily oral dose of 30 g prebiotic supplement (Hangzhou Niuqu Biotech Co., Hainengbo, China) containing fructooligosaccharide (25%), xylooligosaccharide (25%), polydextrose (25%), and resistant dextrin (25%) for 7 d from hospitalization to the day before the operation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 4; Table 3
Description: Differential microbial abundance between patients who took prebiotics and patients who did not
Abundance in Group 1: decreased abundance in colorectal cancer patients who took prebiotics (preoperative fecal sample)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Enterococcus |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Signature 2
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 4; Table 3
Description: Differential microbial abundance between patients who took prebiotics and patients who did not
Abundance in Group 1: increased abundance in colorectal cancer patients who took prebiotics (preoperative fecal sample)
NCBI | Quality Control | Links |
---|---|---|
Bifidobacterium |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Experiment 2
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients non-prebiotic (preoperative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients non-prebiotic (postoperative)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and did not take prebiotics pre-surgery.
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no treatment with antibiotics within 6 mo before surgery
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 5
Description: Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics
Abundance in Group 1: decreased abundance in colorectal cancer patients non-prebiotic (postoperative)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Signature 2
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 5
Description: Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics
Abundance in Group 1: increased abundance in colorectal cancer patients non-prebiotic (postoperative)
NCBI | Quality Control | Links |
---|---|---|
Bacillus | ||
Enterococcus | ||
Lactococcus | ||
Streptococcus |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Experiment 3
Curated date: 2022/09/03
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients who took prebiotics (preoperative fecal sample)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients who took prebiotics (postoperative fecal sample)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and took prebiotics pre-surgery.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 5; Figure 3
Description: Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics
Abundance in Group 1: increased abundance in
NCBI | Quality Control | Links |
---|---|---|
Bacillus | ||
Bifidobacterium | ||
Enterococcus | ||
Escherichia/Shigella sp. |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Signature 2
Curated date: 2022/09/03
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
Source: Table 5; Figure 3
Description: Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics
Abundance in Group 1: decreased abundance in
NCBI | Quality Control | Links |
---|---|---|
Bacteroides |
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks