Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Yang TW, Lee WH, Tu SJ, Huang WC, Chen HM, Sun TH, Tsai MC, Wang CC, Chen HY, Huang CC, Shiu BH, Yang TL, Huang HT, Chou YP, Chou CH, Huang YR, Sun YR, Liang C, Lin FM, Ho SY, Chen WL, Yang SF, Ueng KC, Huang HD, Huang CN, Jong YJ, Lin CC
Journal
Scientific reports
Year
2019
The dysbiosis of human gut microbiota is strongly associated with the development of colorectal cancer (CRC). The dysbiotic features of the transition from advanced polyp to early-stage CRC are largely unknown. We performed a 16S rRNA gene sequencing and enterotype-based gut microbiota analysis study. In addition to Bacteroides- and Prevotella-dominated enterotypes, we identified an Escherichia-dominated enterotype. We found that the dysbiotic features of CRC were dissimilar in overall samples and especially Escherichia-dominated enterotype. Besides a higher abundance of Fusobacterium, Enterococcus, and Aeromonas in all CRC faecal microbiota, we found that the most notable characteristic of CRC faecal microbiota was a decreased abundance of potential beneficial butyrate-producing bacteria. Notably, Oscillospira was depleted in the transition from advanced adenoma to stage 0 CRC, whereas Haemophilus was depleted in the transition from stage 0 to early-stage CRC. We further identified 7 different CAGs by analysing bacterial clusters. The abundance of microbiota in cluster 3 significantly increased in the CRC group, whereas that of cluster 5 decreased. The abundance of both cluster 5 and cluster 7 decreased in the Escherichia-dominated enterotype of the CRC group. We present the first enterotype-based faecal microbiota analysis. The gut microbiota of colorectal neoplasms can be influenced by its enterotype.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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
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
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
CRC
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
CRC positive during colonoscopy
Group 0 sample size Number of subjects in the control (unexposed) group
104
Group 1 sample size Number of subjects in the case (exposed) group
62
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

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)
0.01
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 4A, Text

Description: Differential microbial abundance between controls and colorectal cancer patients

Abundance in Group 1: increased abundance in CRC

NCBI Quality ControlLinks
Aeromonas
Fusobacterium

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 4A, Text

Description: Differential microbial abundance between controls and colorectal cancer patients

Abundance in Group 1: decreased abundance in CRC

NCBI Quality ControlLinks
Bacteroides
Bilophila
Citrobacter
Cronobacter
Dorea
Eubacterium
Roseburia

Revision editor(s): Claregrieve1, WikiWorks