Tumour-associated and non-tumour-associated microbiota in colorectal cancer

Study information

Reviewed Marked as Reviewed by Chinelsy on 2023-10-30

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

26992426

DOI Digital object identifier for electronic documents.

10.1136/gutjnl-2015-309595

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/

Authors

Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F, O'Toole PW

Journal

Gut

Year

2017

Keywords:

COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY

OBJECTIVE: A signature that unifies the colorectal cancer (CRC) microbiota across multiple studies has not been identified. In addition to methodological variance, heterogeneity may be caused by both microbial and host response differences, which was addressed in this study. DESIGN: We prospectively studied the colonic microbiota and the expression of specific host response genes using faecal and mucosal samples ('ON' and 'OFF' the tumour, proximal and distal) from 59 patients undergoing surgery for CRC, 21 individuals with polyps and 56 healthy controls. Microbiota composition was determined by 16S rRNA amplicon sequencing; expression of host genes involved in CRC progression and immune response was quantified by real-time quantitative PCR. RESULTS: The microbiota of patients with CRC differed from that of controls, but alterations were not restricted to the cancerous tissue. Differences between distal and proximal cancers were detected and faecal microbiota only partially reflected mucosal microbiota in CRC. Patients with CRC can be stratified based on higher level structures of mucosal-associated bacterial co-abundance groups (CAGs) that resemble the previously formulated concept of enterotypes. Of these, Bacteroidetes Cluster 1 and Firmicutes Cluster 1 were in decreased abundance in CRC mucosa, whereas Bacteroidetes Cluster 2, Firmicutes Cluster 2, Pathogen Cluster and Prevotella Cluster showed increased abundance in CRC mucosa. CRC-associated CAGs were differentially correlated with the expression of host immunoinflammatory response genes. CONCLUSIONS: CRC-associated microbiota profiles differ from those in healthy subjects and are linked with distinct mucosal gene-expression profiles. Compositional alterations in the microbiota are not restricted to cancerous tissue and differ between distal and proximal cancers.

Experiment 1

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Curated date: 2022/01/26

Curator: Itslanapark

Revision editor(s): WikiWorks, Itslanapark, Peace Sandy, ChiomaBlessing, Chinelsy

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: Intestinal mucosa Bowel mucosa,Bowel mucosa of organ,Bowel mucous membrane,Bowel organ mucosa,Intestine mucosa,Intestine mucosa of organ,Intestine mucous membrane,Intestine organ mucosa,Mucosa of bowel,Mucosa of intestine,Mucosa of organ of bowel,Mucosa of organ of intestine,Mucous membrane of bowel,Mucous membrane of intestine,Organ mucosa of bowel,Organ mucosa of intestine,Tunica mucosa intestini,Intestinal mucosa,intestinal mucosa

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: colorectal cancer (CRC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The patients undergoing surgery for CRC have confirmed CRC.

Group 0 sample size Number of subjects in the control (unexposed) group: 56

Group 1 sample size Number of subjects in the case (exposed) group: 59

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).: 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)?: Yes

Matched on Factors on which subjects have been matched on in a case-control study: age

Signature 1

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Reviewed Marked as Reviewed by Chinelsy on 2023-10-30

Curated date: 2023/10/19

Curator: Chinelsy

Revision editor(s): Chinelsy, ChiomaBlessing, WikiWorks

Source: Supplementary File: Table S3 and Table S4

Description: Differential mucosal microbiota composition of patients with CRC compared to healthy controls

Abundance in Group 1: increased abundance in colorectal cancer (CRC)

NCBI	Quality Control	Links
Actinomyces
Alistipes
Allisonella
Bacteroides
Bacteroidetes incertae sedis
Bifidobacterium
Dialister
Enterococcus
Escherichia/Shigella sp.
Fusobacterium
Gemella
Granulicatella
Lachnospiraceae incertae sedis
Mogibacterium
Oscillibacter
Parvimonas
Peptostreptococcus
Phascolarctobacterium
Pseudomonas
Roseburia
Ruminococcus
Staphylococcus
Streptococcus
Victivallis
unclassified Clostridium
unclassified Eubacteriales
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Oxalobacteraceae
Acetanaerobacterium
Campylobacter
Eubacterium
Howardella
Porphyromonas
Prevotella
unclassified Porphyromonadaceae

Revision editor(s): Chinelsy, ChiomaBlessing, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-2

Curated date: 2024/02/02

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, WikiWorks

Source: Supplementary File: Table S3

Description: Differential mucosal microbiota composition of patients with CRC compared to healthy controls

Abundance in Group 1: decreased abundance in colorectal cancer (CRC)

NCBI	Quality Control	Links
Anaerorhabdus
Anaerostipes
Bacteroides
Blautia
Butyricicoccus
Coprococcus
Dialister
Dorea
Erysipelotrichaceae incertae sedis
Faecalibacterium
Gemmiger
Holdemania
Klebsiella
Lachnospiraceae incertae sedis
Roseburia
unclassified Bacillota
unclassified Clostridium
unclassified Lachnospiraceae
unclassified Oscillospiraceae

Revision editor(s): ChiomaBlessing, WikiWorks

Experiment 3

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Curated date: 2024/02/02

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Distal (and rectal) cancer

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

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