Metagenomic analyses of the gut microbiota associated with colorectal adenoma

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

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

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 4B

Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.

Abundance in Group 1: decreased abundance in Intramucosal CRC

NCBI	Links
Megamonas
Sphingobium ⚠

Revision editor(s): Jeshudy

Signature 2

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 4B

Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.

Abundance in Group 1: increased abundance in Intramucosal CRC

NCBI	Links
Actinobacillus
Fusobacterium
Parvimonas
Peptostreptococcus
Actinomyces

Revision editor(s): Jeshudy

Signature 3

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 7

Description: Characterization of Fusobacterium spp. in intramucosal CRC patients and healthy subjects. (A) Histogram of the LDA scores (log10) computed for Fusobacterium spp. Features that were differentially abundant in intramucosal CRC and healthy subjects. (B) Relative abundances of the groups of Fusobacterium spp. displaying significant differences between intramucosal CRC and healthy subjects.

Abundance in Group 1: decreased abundance in Intramucosal CRC

NCBI	Links
Fusobacterium periodonticum
Fusobacterium perfoetens

Revision editor(s): Jeshudy

Signature 4

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 7

Description: Characterization of Fusobacterium spp. in intramucosal CRC patients and healthy subjects. (A) Histogram of the LDA scores (log10) computed for Fusobacterium spp. Features that were differentially abundant in intramucosal CRC and healthy subjects. (B) Relative abundances of the groups of Fusobacterium spp. displaying significant differences between intramucosal CRC and healthy subjects.

Abundance in Group 1: increased abundance in Intramucosal CRC

NCBI	Links
Fusobacterium varium

Revision editor(s): Jeshudy

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

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: CRA (colorectal adenoma)
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: 47
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

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

Needs review

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

NCBI	Links
Butyricimonas
Collinsella
Mitsuokella
Deltaproteobacteria
Desulfovibrionales
Synergistaceae
Comamonas ⚠
Desulfovibrionaceae

Revision editor(s): Jeshudy

Signature 2

Needs review

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: decreased abundance in Intramucosal CRC

NCBI	Links
Megamonas
Erysipelotrichaceae

Revision editor(s): Jeshudy

Signature 3

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 9

Description: Histogram of the gut microbiota relative abundances in patients with CRA and intramucosal CRC. Relative abundances of the groups of bacteria that displayed significant differences between CRA patients and healthy subjects

Abundance in Group 1: increased abundance in Intramucosal CRC

NCBI	Links
Collinsella
Deltaproteobacteria
Desulfovibrionales
Synergistaceae
Erysipelotrichaceae

Revision editor(s): Jeshudy

Signature 4

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 9

Description: Histogram of the gut microbiota relative abundances in patients with CRA and intramucosal CRC. Relative abundances of the groups of bacteria that displayed significant differences between CRA patients and healthy subjects

Abundance in Group 1: decreased abundance in Intramucosal CRC

NCBI	Links
Veillonella

Revision editor(s): Jeshudy

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

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 (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: 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
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

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

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 2B

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: decreased abundance in CRA (colorectal adenoma)

NCBI	Links
Lachnobacterium
Butyricimonas
Salmonella ⚠
Comamonas ⚠
Moraxellaceae

Revision editor(s): Jeshudy

Signature 2

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 2B

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: increased abundance in CRA (colorectal adenoma)

NCBI	Links
Atopobium
Parvimonas
Fusobacterium

Revision editor(s): Jeshudy

Signature 3

Needs review

Curated date: 2022/07/04

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 6

Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.

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

NCBI	Links
Fusobacterium periodonticum
Fusobacterium nucleatum

Revision editor(s): Jeshudy

Signature 4