Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer

Study information

Needs review

study design

case-control
integrative analysisStudy design: "integrative analysis" is not in the list (case-control, cross-sectional observational, not case-control, time series / longitudinal observational, laboratory experiment, randomized controlled trial, prospective cohort, meta-analysis) of allowed values.

Citation

PMID PubMed identifier for scientific articles.

32370168

DOI Digital object identifier for electronic documents.

10.3390/cancers12051142

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281174/

Authors

Clos-Garcia M, Garcia K, Alonso C, Iruarrizaga-Lejarreta M, D'Amato M, Crespo A, Iglesias A, Cubiella J, Bujanda L, Falcón-Pérez JM

Journal

Cancers

Year

2020

Keywords:

integration, metabolomics, microbiome, multiomics, omics, omics integration

Although colorectal cancer (CRC) is the second leading cause of death in developed countries, current diagnostic tests for early disease stages are suboptimal. We have performed a combination of UHPLC-MS metabolomics and 16S microbiome analyses on 224 feces samples in order to identify early biomarkers for both advanced adenomas (AD) and CRC. We report differences in fecal levels of cholesteryl esters and sphingolipids in CRC. We identified Fusobacterium, Parvimonas and Staphylococcus to be increased in CRC patients and Lachnospiraceae family to be reduced. We finally described Adlercreutzia to be more abundant in AD patients' feces. Integration of metabolomics and microbiome data revealed tight interactions between bacteria and host and performed better than FOB test for CRC diagnosis. This study identifies potential early biomarkers that outperform current diagnostic tools and frame them into the stablished gut microbiota role in CRC pathogenesis.

Experiment 1

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Reviewed Marked as Reviewed by Rimsha on 2022/05/15

Curated date: 2021/12/17

Curator: Itslanapark

Revision editor(s): Rimsha, Itslanapark, WikiWorks, Peace Sandy

Subjects

Location of subjects: Spain

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: CRC patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients with gastrointestinal symptoms referred for colonoscopy

Group 0 sample size Number of subjects in the control (unexposed) group: 77

Group 1 sample size Number of subjects in the case (exposed) group: 89

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): none

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V2

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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Reviewed Marked as Reviewed by Rimsha on 2022/05/15

Curated date: 2022/01/02

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 4B

Description: Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.

Abundance in Group 1: increased abundance in CRC patients

NCBI	Quality Control	Links
Fusobacterium
Parvimonas
Staphylococcus

Revision editor(s): Itslanapark

Signature 2

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Reviewed Marked as Reviewed by Rimsha on 2022/05/15

Curated date: 2022/01/02

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 4B

Description: Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.

Abundance in Group 1: decreased abundance in CRC patients

NCBI	Quality Control	Links
Blautia
Clostridium
Coprococcus
Streptococcus

Revision editor(s): Itslanapark

Experiment 2

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Reviewed Marked as Reviewed by Rimsha on 2022/05/15

Curated date: 2022/05/15

Curator: Rimsha

Revision editor(s): Rimsha, WikiWorks

Differences from previous experiment shown

Subjects

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

Group 0 sample size Number of subjects in the control (unexposed) group: 65

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified