Metagenomic analyses of the gut microbiota associated with colorectal adenoma/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks

Subjects

Location of subjects
Japan
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
Intestine Bowel,Intestinal tract,Intestine,intestine
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
Healthy
Group 1 name Corresponds to the case (exposed) group for case-control studies
CRA (colorectal adenoma)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colorectal adenoma, as diagnosed after a complete colonoscopic exampination
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
47
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None Specified

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

Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy, Atrayees

Source: Figure 2B, Figure 6

Description: Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. (A) Taxonomic representation of statistically and biologically consistent differences in CRA and healthy subjects. (B) Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.

Abundance in Group 1: increased abundance in CRA (colorectal adenoma)

NCBI Quality ControlLinks
Lachnobacterium
Butyricimonas
Salmonella
Comamonas
Moraxellaceae
Fusobacterium varium

Revision editor(s): Jeshudy, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy, Atrayees

Source: Figure 2B, Figure 6

Description: Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.

Abundance in Group 1: decreased abundance in CRA (colorectal adenoma)

NCBI Quality ControlLinks
Atopobium
Parvimonas
Fusobacterium
Fusobacterium periodonticum
Fusobacterium nucleatum
Fusobacteriia
Fusobacteriales
Fusobacteriaceae

Revision editor(s): Jeshudy, Atrayees