Metagenomic analyses of the gut microbiota associated with colorectal adenoma

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

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Subjects

Location of subjects: Japan

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Intestine Bowel,Intestinal tract,Intestine

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: intramucosal CRCintramucosal CRC

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: Intramucosal CRC
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum
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: 24
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: unchanged

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 4B, Figure 7

Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects.

Abundance in Group 1: decreased abundance in Intramucosal CRC

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Megamonas
Sphingobium
Fusobacterium periodonticum
Fusobacterium perfoetens

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 4B, Figure 7

Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects.

Abundance in Group 1: increased abundance in Intramucosal CRC

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Actinobacillus
Fusobacterium
Parvimonas
Peptostreptococcus
Actinomyces
Fusobacteriia
Fusobacteriales
Fusobacteriaceae
Fusobacterium varium

Revision editor(s): Jeshudy, Atrayees

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: CRA (colorectal adenoma)
Group 0 sample size Number of subjects in the control (unexposed) group: 47

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

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

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 8B

Description: Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.

Abundance in Group 1: increased abundance in Intramucosal CRC

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Butyricimonas
Collinsella
Mitsuokella
Deltaproteobacteria
Desulfovibrionales
Synergistaceae
Comamonas
Desulfovibrionaceae

Revision editor(s): Jeshudy

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 8B, Figure 9

Description: Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.

Abundance in Group 1: decreased abundance in Intramucosal CRC

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Megamonas
Erysipelotrichaceae
Veillonella

Revision editor(s): Jeshudy, Atrayees

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks

Differences from previous experiment shown

Subjects

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

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

Lab analysis

Statistical Analysis

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)

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Lachnobacterium
Butyricimonas
Salmonella
Comamonas
Moraxellaceae
Fusobacterium varium

Revision editor(s): Jeshudy, Atrayees

Signature 2