A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/28

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Fatima, Rimsha, Mary Bearkland, Peace Sandy

Subjects

Location of subjects: China

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 adenocarcinoma adenocarcinoma of large bowel,adenocarcinoma of large intestine,adenocarcinoma of the large bowel,adenocarcinoma of the large intestine,colorectal (colon or rectal) adenocarcinoma,colorectal adenocarcinoma,colorectum adenocarcinoma,large bowel adenocarcinoma,large intestine adenocarcinoma,Colorectal adenocarcinoma

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: diagnosed of colorectal cancer by colonoscopy and histopathology

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 44

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Alpha Diversity

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

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figures 4b

Description: Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed from features differentially abundant in CRC and HC fecal samples. The criteria for feature selection were LDA score > 4, p < 0.05, Green and red represent the HC group and CRC group, respectively.

Abundance in Group 1: increased abundance in colorectal cancer patients

NCBI	Quality Control	Links
Bacteroides
Bifidobacterium
Shigella
Escherichia

Revision editor(s): Mary Bearkland

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Fatima

Source: Figures 4b

Description: Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed from features differentially abundant in CRC and HC fecal samples. The criteria for feature selection were LDA score > 4, p < 0.05, Green and red represent the HC group and CRC group, respectively.

Abundance in Group 1: decreased abundance in colorectal cancer patients

NCBI	Quality Control	Links
Collinsella
Coprobacillus
Faecalibacterium
Romboutsia
Streptococcus
Agathobacter

Revision editor(s): Mary Bearkland, Fatima

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/28

Curator: Mary Bearkland

Revision editor(s): WikiWorks, LGeistlinger, Fatima, Mary Bearkland, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: colorectal cancer patients without KRAS mutation

Group 1 name Corresponds to the case (exposed) group for case-control studies: colorectal cancer patients with KRAS mutation

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 18

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/31

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Fatima, Merit

Source: Figure 5a

Description: LEfSe was used to compare the microbial variation of the KRAS

Abundance in Group 1: increased abundance in colorectal cancer patients with KRAS mutation

NCBI	Quality Control	Links
Acidaminococcaceae
Alistipes sp.
Anaerobutyricum hallii
Bacillota
Butyricicoccus
Caproiciproducens
Enterocloster bolteae
Faecalibacterium
Gracilibacter
Harryflintia
Harryflintia acetispora
Holdemania filiformis
Lachnoclostridium
Lachnoclostridium edouardi
Lachnospiraceae
Megamonas
Novosphingobium
Phascolarctobacterium
Roseburia
Roseburia sp. 11SE38
Sphingomonadaceae
Sphingomonadales
unclassified Anaerobutyricum
unclassified Butyricicoccus
unclassified Caproiciproducens
unclassified Coprococcus
unclassified Faecalibacterium
unclassified Megamonas
unclassified Phascolarctobacterium
uncultured Eubacterium sp.
uncultured Gracilibacter sp.
uncultured Prevotella sp.

Revision editor(s): Mary Bearkland, Fatima, Merit

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/10/20

Curated date: 2022/08/31

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Fatima

Source: Figure 5a

Description: LEfSe was used to compare the microbial variation of the KRAS

Abundance in Group 1: decreased abundance in colorectal cancer patients with KRAS mutation

NCBI	Quality Control	Links
Actinomycetota
Bacteria
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Bifidobacterium dentium
Bifidobacterium longum
Bifidobacterium pseudocatenulatum
Enterobacterales
Enterobacteriaceae
Lactobacillus sp. T17/4F
uncultured Bifidobacterium sp.
Bifidobacterium catenulatum subsp. kashiwanohense

Revision editor(s): Mary Bearkland, Fatima

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/02

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Atrayees, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: colorectal cancer patients without TP53 mutation

Group 1 name Corresponds to the case (exposed) group for case-control studies: colorectal cancer patients with TP53 mutation

Group 0 sample size Number of subjects in the control (unexposed) group: 11

Group 1 sample size Number of subjects in the case (exposed) group: 28

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/02

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 5b

Description: LEfSe was used to compare the microbial variation of the TP53

Abundance in Group 1: increased abundance in colorectal cancer patients with TP53 mutation

NCBI	Quality Control	Links
Eubacterium coprostanoligenes

Revision editor(s): Mary Bearkland

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/02

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Merit, Atrayees

Source: Figure 5b

Description: LEfSe was used to compare the microbial variation of the TP53

Abundance in Group 1: decreased abundance in colorectal cancer patients with TP53 mutation

NCBI	Quality Control	Links
Oscillospiraceae
unclassified Oscillospiraceae

Revision editor(s): Mary Bearkland, Merit, Atrayees

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/02

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Atrayees, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: colorectal cancer patients without APC mutation

Group 1 name Corresponds to the case (exposed) group for case-control studies: colorectal cancer patients with APC mutation

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: diagnosed with colorectal cancer by colonoscopy and histopathology

Group 0 sample size Number of subjects in the control (unexposed) group: 9

Group 1 sample size Number of subjects in the case (exposed) group: 30

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/03

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 5c

Description: LEfSe was used to compare the microbial variation of the APC groups.

Abundance in Group 1: increased abundance in colorectal cancer patients with APC mutation

NCBI	Quality Control	Links
Actinomyces
Actinomycetaceae
Actinomycetales

Revision editor(s): Mary Bearkland

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/02

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Atrayees, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: colorectal cancer patients without PIK3CA mutation

Group 1 name Corresponds to the case (exposed) group for case-control studies: colorectal cancer patients with PIK3CA mutation

Group 0 sample size Number of subjects in the control (unexposed) group: 33

Group 1 sample size Number of subjects in the case (exposed) group: 6

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-19

Curated date: 2022/09/03

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 5d

Description: LEfSe was used to compare the microbial variation of the PIK3CA groups.

Abundance in Group 1: decreased abundance in colorectal cancer patients with PIK3CA mutation

NCBI	Quality Control	Links
Actinomycetales
unclassified Actinomyces
Actinomycetaceae
Actinomyces

Revision editor(s): Mary Bearkland

Signature 2