Dysbiosis of human gut microbiome in young-onset colorectal cancer
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X, Ma Y
Journal
Nature communications
Year
2021
The incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 310 samples is used to validate the results. Furthermore, species-level and functional analysis are performed by metagenome sequencing using 200 samples. Gut microbial diversity is increased in yCRC. Flavonifractor plautii is an important bacterial species in yCRC, while genus Streptococcus contains the key phylotype in the old-onset colorectal cancer. Functional analysis reveals that yCRC has unique characteristics of bacterial metabolism characterized by the dominance of DNA binding and RNA-dependent DNA biosynthetic process. The random forest classifier model achieves a powerful classification potential. This study highlights the potential of the gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with yCRC.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Curated date: 2022/06/24
Curator: Jeshudy
Revision editor(s): WikiWorks, Claregrieve1, Jeshudy, 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
- yControl
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- yCRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- young-onset CRC patients (<50 years old)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 148
- Group 1 sample size Number of subjects in the case (exposed) group
- 144
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Source: Figure 3B
Description: Differential microbial abundance between yCRC and yControl groups
Abundance in Group 1: increased abundance in yCRC
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Flavonifractor | ||
| Flavonifractor plautii | ||
| Fusobacterium | ||
| Lachnospiraceae | ||
| Odoribacter | ||
| Veillonella |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Source: Figure 3B
Description: Differential microbial abundance between yCRC and yControl groups
Abundance in Group 1: decreased abundance in yCRC
Revision editor(s): Jeshudy, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Curated date: 2022/06/24
Curator: Jeshudy
Revision editor(s): WikiWorks, Claregrieve1, Jeshudy, Victoria
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- oControls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oCRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- old-onset CRC patients (50 years old or older)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 203
- Group 1 sample size Number of subjects in the case (exposed) group
- 233
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Source: Figure 3A
Description: Differential microbial abundance between oCRC and oControl groups
Abundance in Group 1: decreased abundance in oCRC
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/11
Source: Figure 3A
Description: Differential microbial abundance between oCRC and oControl groups
Abundance in Group 1: increased abundance in oCRC
Revision editor(s): Jeshudy, Claregrieve1
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