Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis
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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.
Authors
Jin M, Fan Q, Shang F, Zhang T, Ogino S, Liu H
Journal
Oncology letters
Year
2024
Keywords:
colorectal cancer, fusobacteria, gut microbiota, liver metastasis
Liver metastasis is a major cause of mortality in patients with advanced stages of colorectal cancer (CRC). The gut microbiota has been demonstrated to influence the progression of liver diseases, potentially providing novel perspectives for diagnosis, treatment and research. However, the gut microbial characteristics in CRC with liver metastasis (LM) and with no liver metastasis (NLM) have not yet been fully established. In the present study, high-throughput 16S RNA sequencing technology was employed, in order to examine the gut microbial richness and composition in patients with CRC with LM or NLM. A discovery cohort (cohort 2; LM=18; NLM=36) and a validation cohort (cohort 3; LM=13; NLM=41) were established using fresh feces. In addition, primary carcinoma tissue samples were also analyzed (LM=8 and NLM=10) as a supplementary discovery cohort (cohort 1). The findings of the present study indicated that the intestinal microbiota richness and diversity were increased in the LM group as compared to the NLM group. A significant difference was observed in species composition between the LM and NLM group. In the two discovery cohorts with two different samples, the dominant phyla were consistent, but varied at lower taxonomic levels. Phylum Fusobacteria presented consistent and significant enrichment in LM group in both discovery cohorts. Furthermore, with the application of a random forest model and receiver operator characteristic curve analysis, Fusobacteria was identified as a potential biomarker for LM. Moreover, Fusobacteria was also a poor prognosis factor for survival. Importantly, the findings were reconfirmed in the validation cohort. On the whole, the findings of the present study demonstrated that CRC with LM and NLM exhibit distinct gut microbiota characteristics. Fusobacteria detection thus has potential for use in predicting LM and a poor prognosis of patients with CRC.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
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
- Colorectum Colorectum,colorectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Metastatic colorectal cancer Metastatic colorectal cancer,metastatic colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No liver metastasis (NLM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Liver metastasis (LM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal patients with liver metastasis (LM) in the supplementary discovery cohort (cohort 1)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within 3 months prior to specimen collection.
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4a, 4b and Figure 5c
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.
Abundance in Group 1: increased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4a, 4b and Figure 5c
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.
Abundance in Group 1: decreased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Differences from previous experiment shown
Subjects
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal patients with liver metastasis (LM) in the discovery cohort (cohort 2)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4c, 4d and Figure 5d
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.
Abundance in Group 1: increased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4c, 4d and Figure 5d
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.
Abundance in Group 1: decreased abundance in Liver metastasis (LM)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidobacteriota | ||
| Actinomycetota | ||
| Deinococcota | ||
| Mycoplasmatota | ||
| Nitrospirota | ||
| Porphyromonas | ||
| Pseudomonadota |
Revision editor(s): Aleru Divine
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4e, 4f and Figure 5e
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.
Abundance in Group 1: increased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-3
Source: Figure 4e, 4f and Figure 5e
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.
Abundance in Group 1: decreased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
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