Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

22622349

DOI Digital object identifier for electronic documents.

10.1038/ismej.2012.43

URI

https://pubmed.ncbi.nlm.nih.gov/22622349/

Authors

Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, Randall TA, Galanko J, Benson A, Sandler RS, Rawls JF, Abdo Z, Fodor AA, Keku TO

Journal

The ISME journal

Year

2012

Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1-V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.

Experiment 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6

Curated date: 2024/03/15

Curator: Fetlework

Revision editor(s): Fetlework, Rahila

Subjects

Location of subjects: United States of America

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: Colorectal mucosa Colorectal mucosa,colorectal mucosa

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients who have colorectal adenoma

Group 0 sample size Number of subjects in the control (unexposed) group: 38

Group 1 sample size Number of subjects in the case (exposed) group: 33

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Subjects were asked if they used antibiotics in the last 3 months before colonoscopy. In all, 33 subjects (11 controls and 22 cases) answered the question. Among these subjects, one case subject (4.55%) and one control subject (9.09%) reported antibiotics use.

Lab analysis

Sequencing type: 16S

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

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

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

Alpha Diversity

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

Richness Number of species: increased

Signature 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6

Curated date: 2024/05/01

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Source: Supplementary Table 1 and 2

Description: Wilcoxon-tests on log-normalized abundances of of all phyla and genera in cases (33 subjects) versus controls (38 subjects).

Abundance in Group 1: increased abundance in Adenoma patients (cases)

NCBI	Quality Control	Links
Acidobacteriota
Acidovorax
Acinetobacter
Cloacibacterium
Agrobacterium
Akkermansia
Aquabacterium
Azonexus
Cyanobacteriota
Dechloromonas
Delftia
Helicobacter
Lactobacillus
Lactococcus
Leuconostoc
Marvinbryantia
Sphingobium
Stenotrophomonas
Succinivibrio
Turicibacter
Verrucomicrobiota
Weissella
TM7TM7

Revision editor(s): Rahila, Scholastica