Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer/Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2022/06/12

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

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
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
healthy control (normal and a few polyps)
Group 1 name Corresponds to the case (exposed) group for case-control studies
stage I/II (SI/II)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
stage I and II CRCs
Group 0 sample size Number of subjects in the control (unexposed) group
251
Group 1 sample size Number of subjects in the case (exposed) group
111
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
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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)
0.005
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes


Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2022/06/12

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 2B

Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).

Abundance in Group 1: increased abundance in stage I/II (SI/II)

NCBI Quality ControlLinks
Collinsella aerofaciens
Fusobacterium nucleatum
Gemella morbillorum
Lancefieldella parvula
Parvimonas micra
Peptostreptococcus anaerobius
Peptostreptococcus stomatis
Porphyromonas uenonis
Schaalia odontolytica
Solobacterium moorei

Revision editor(s): Jeshudy

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2022/06/12

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 2B

Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).

Abundance in Group 1: decreased abundance in stage I/II (SI/II)

NCBI Quality ControlLinks
Bifidobacterium longum subsp. longum
Lachnospira eligens
Lachnospira multipara

Revision editor(s): Jeshudy