Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer/Experiment 1
Curated date: 2022/01/26
Curator: Itslanapark
Revision editor(s): Chloe, Itslanapark, WikiWorks, 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
- 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
- Healthy Controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- 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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Curated date: 2022/01/31
Curator: Itslanapark
Revision editor(s): Chloe, Itslanapark, Aiyshaaaa, Merit
Source: Figure 4C
Description: Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.
Abundance in Group 1: increased abundance in CRC
Revision editor(s): Chloe, Itslanapark, Aiyshaaaa, Merit
Signature 2
Source: Figure 4c
Description: Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.
Abundance in Group 1: decreased abundance in CRC
Revision editor(s): Fatima, Chloe, Itslanapark, Merit
