The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
Uterus Uterus,uterus
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Ovarian cancer cancer of ovary,cancer of the ovary,malignant neoplasm of ovary,malignant neoplasm of the ovary,malignant ovarian neoplasm,malignant ovarian tumor,malignant ovary neoplasm,malignant tumor of ovary,malignant tumor of the ovary,malignant tumour of ovary,ovarian cancer,ovarian cancer, epithelial,ovarian malignant tumor,ovarian neoplasm,ovary cancer,ovary neoplasm,primary ovarian cancer,tumor of the ovary,Ovarian cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
normal tissue
Group 1 name Corresponds to the case (exposed) group for case-control studies
ovarian cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
women diagnosed with high grade ovarian cancer
Group 0 sample size Number of subjects in the control (unexposed) group
25
Group 1 sample size Number of subjects in the case (exposed) group
25
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months

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
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
3.5

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
unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 2, Fig S3

Description: LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.

Abundance in Group 1: increased abundance in ovarian cancer

NCBI Quality ControlLinks
Pseudomonadota
Enhydrobacter
Comamonas
Staphylococcus
Sphingobium
Methylobacterium
Cupriavidus
Providencia
Caldimonas
Sediminibacterium
Acidovorax
Sphingomonas
Acinetobacter
Moraxella osloensis
Sphingobium yanoikuyae
Providencia vermicola
Acinetobacter lwoffii
Sphingomonas azotifigens

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 2, Fig S3

Description: LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.

Abundance in Group 1: decreased abundance in ovarian cancer

NCBI Quality ControlLinks
Bacillota
Actinomycetota
Acidobacteriota
Fastidiosipila
Lactococcus
Lactococcus piscium

Revision editor(s): WikiWorks, Peace Sandy