Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing/Experiment 4

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Subjects

Location of subjects
Norway
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 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 controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
HRA (high-risk adenoma)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.
Group 0 sample size Number of subjects in the control (unexposed) group
53
Group 1 sample size Number of subjects in the case (exposed) group
63

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).
raw counts
Statistical test
Negative Binomial Regression
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)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age, time, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, geographic area

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between HRA and healthy controls.

Abundance in Group 1: increased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Lacrimispora saccharolytica

Revision editor(s): Yjung24, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-24

Curated date: 2023/10/22

Curator: Yjung24

Revision editor(s): Yjung24, Folakunmi

Source: Table 2

Description: Differential abundance analyses of taxa and pathways between HRA and healthy controls.

Abundance in Group 1: decreased abundance in HRA (high-risk adenoma)

NCBI Quality ControlLinks
Parasutterella

Revision editor(s): Yjung24, Folakunmi