The human gut microbiome as a screening tool for colorectal cancer

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

25104642

DOI Digital object identifier for electronic documents.

10.1158/1940-6207.CAPR-14-0129

URI

Authors

Zackular JP, Rogers MA, Ruffin MT, Schloss PD

Journal

Cancer prevention research (Philadelphia, Pa.)

Year

2014

Recent studies have suggested that the gut microbiome may be an important factor in the development of colorectal cancer. Abnormalities in the gut microbiome have been reported in patients with colorectal cancer; however, this microbial community has not been explored as a potential screen for early-stage disease. We characterized the gut microbiome in patients from three clinical groups representing the stages of colorectal cancer development: healthy, adenoma, and carcinoma. Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas. Combined with known clinical risk factors of colorectal cancer (e.g., BMI, age, race), data from the gut microbiome significantly improved the ability to differentiate between healthy, adenoma, and carcinoma clinical groups relative to risk factors alone. Using Bayesian methods, we determined that using gut microbiome data as a screening tool improved the pretest to posttest probability of adenoma more than 50-fold. For example, the pretest probability in a 65-year-old was 0.17% and, after using the microbiome data, this increased to 10.67% (1 in 9 chance of having an adenoma). Taken together, the results of our study demonstrate the feasibility of using the composition of the gut microbiome to detect the presence of precancerous and cancerous lesions. Furthermore, these results support the need for more cross-sectional studies with diverse populations and linkage to other stool markers, dietary data, and personal health information.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: United States of America; Canada

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

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy control

Group 1 name Corresponds to the case (exposed) group for case-control studies: carcinoma

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: carcinoma

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 30

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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: 2.5

Signature 1

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Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Supplemental Figure 2 and text

Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.

Abundance in Group 1: increased abundance in carcinoma

NCBI	Quality Control	Links
Fusobacterium
Porphyromonas
Lachnospiraceae
Enterobacteriaceae

Revision editor(s): WikiWorks

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Supplemental Figure 2 and text

Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.

Abundance in Group 1: decreased abundance in carcinoma

NCBI	Quality Control	Links
Bacteroides
Lachnospiraceae
Eubacteriales

Revision editor(s): WikiWorks