Gut microbiota display alternative profiles in patients with early-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
Xiong H, Wang J, Chang Z, Hu H, Yuan Z, Zhu Y, Hu Z, Wang C, Liu Y, Wang Y, Wang G, Tang Q
Journal
Frontiers in cellular and infection microbiology
Year
2022
Keywords:
16S rRNA, colorectal cancer, early onset, functional annotation, gut microbiota
BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is increasing worldwide. This study aimed to explore whether there is an alternative gut microbiota profile in patients with early-onset colorectal cancer. METHODS: A total of 24 patients with EOCRC, 43 patients with late-onset colorectal cancer and 31 young volunteers were included in this study. The diversity of their fecal bacteria was explored using 16S ribosomal RNA gene sequencing. Cluster of ortholog genes (COG) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) were used to detect enrichment pathways among the three groups. RESULTS: Community separations were observed among the three groups. The Shannon index of the EOCRC group was significantly lower than the LOCRC group (P=0.007) and the NC group (P=0.008). Both PCoA analysis (Principal co-ordinates analysis, P=0.001) and NMDS (non-metric multidimensional scaling, stress=0.167, P=0.001) analysis indicated significant difference in beta diversity among the three groups. Fusobacteria, Bacteroidetes, and Clostridia were the most abundant bacteria in the EOCRC group, LOCRC group, and NC group, respectively. The results of COG showed that transcription (P=0.01398), defense mechanisms (P=0.04304), inorganic ion transport and metabolism (P=0.00225) and cell wall/membrane/envelope biogenesis (P=0.02534) were differentially expressed among the three groups. The KEGG modules involved in membrane transport (P=0.00856) and porphyrin and chlorophyll metabolism (P=0.04909) were differentially expressed among the three groups. CONCLUSION: Early-onset colorectal cancer patients have a different gastrointestinal microbiota derangement compared to late-onset colorectal cancer patients. This dysbiosis can be reflected in the species diversity of the microbiota, the abundance of bacteria, and the abnormal functional predictions.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-4
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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EOCRC (Early-onset Colorectal cancer) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal cancer diagnosed before the age of 50 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months, including probiotics and corticosteroids use.
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
- Kruskall-Wallis
- 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
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol drinking, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-4
Source: Figure 3
Description: Differentially abundant taxa in Early onset colorectal cancer (EOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.
Abundance in Group 1: increased abundance in EOCRC (Early-onset Colorectal cancer) patients
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2023-12-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LOCRC (Late onset colorectal cancer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Late onset colorectal cancer (diagnosed >=50 years of age)
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-4
Source: Figure 3
Description: Differentially abundant taxa in Late onset colorectal cancer (LOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.
Abundance in Group 1: increased abundance in LOCRC (Late onset colorectal cancer)
Revision editor(s): Yjung24, ChiomaBlessing, Folakunmi
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