The oral microbiota in colorectal cancer is distinctive and predictive
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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
Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F, O'Toole PW
Journal
Gut
Year
2018
Keywords:
colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers
BACKGROUND AND AIMS: Microbiota alterations are linked with colorectal cancer (CRC) and notably higher abundance of putative oral bacteria on colonic tumours. However, it is not known if colonic mucosa-associated taxa are indeed orally derived, if such cases are a distinct subset of patients or if the oral microbiome is generally suitable for screening for CRC. METHODS: We profiled the microbiota in oral swabs, colonic mucosae and stool from individuals with CRC (99 subjects), colorectal polyps (32) or controls (103). RESULTS: Several oral taxa were differentially abundant in CRC compared with controls, for example, Streptococcus and Prevotellas pp. A classification model of oral swab microbiota distinguished individuals with CRC or polyps from controls (sensitivity: 53% (CRC)/67% (polyps); specificity: 96%). Combining the data from faecal microbiota and oral swab microbiota increased the sensitivity of this model to 76% (CRC)/88% (polyps). We detected similar bacterial networks in colonic microbiota and oral microbiota datasets comprising putative oral biofilm forming bacteria. While these taxa were more abundant in CRC, core networks between pathogenic, CRC-associated oral bacteria such as Peptostreptococcus, Parvimonas and Fusobacterium were also detected in healthy controls. High abundance of Lachnospiraceae was negatively associated with the colonisation of colonic tissue with oral-like bacterial networks suggesting a protective role for certain microbiota types against CRC, possibly by conferring colonisation resistance to CRC-associated oral taxa and possibly mediated through habitual diet. CONCLUSION: The heterogeneity of CRC may relate to microbiota types that either predispose or provide resistance to the disease, and profiling the oral microbiome may offer an alternative screen for detecting CRC.
Experiment 1
Empty strings are not accepted.
Reviewed Marked as Reviewed by Folakunmi on 2024-1-23
Subjects
- Location of subjects
- Ireland
- 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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma
- 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
- Individuals with CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with CRC
- Group 0 sample size Number of subjects in the control (unexposed) group
- 103
- Group 1 sample size Number of subjects in the case (exposed) group
- 99
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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)?
- Yes
Signature 1
Needs review
Source: Figure 5(B)
Description: Scatterplot of the colonic prevalence of bacterial OTUs associated with oral pathogen and biofilm CAGs.
Abundance in Group 1: increased abundance in Individuals with CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Fusobacterium | ||
| Gemella | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Solobacterium | ||
| Streptococcus |
Experiment 2
Empty strings are not accepted.
Reviewed Marked as Reviewed by Folakunmi on 2024-1-23
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: supplementary table 2
Description: Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM
Abundance in Group 1: increased abundance in Individuals with CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Parvimonas | ||
| Prevotella | ||
| Alloprevotella | ||
| Lachnoanaerobaculum | ||
| Neisseria | ||
| Streptococcus |
Experiment 3
Empty strings are not accepted.
Reviewed Marked as Reviewed by Folakunmi on 2024-1-23
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals with polyps
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with polyps
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Signature 1
Source: supplementary table 2
Description: Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM
Abundance in Group 1: increased abundance in Individuals with polyps
| NCBI | Quality Control | Links |
|---|---|---|
| Parvimonas | ||
| Streptococcus | ||
| Leptotrichia |
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