The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30737418

DOI Digital object identifier for electronic documents.

10.1038/s41598-018-38031-2

URI

Authors

Zhou B, Sun C, Huang J, Xia M, Guo E, Li N, Lu H, Shan W, Wu Y, Li Y, Xu X, Weng D, Meng L, Hu J, Gao Q, Ma D, Chen G

Journal

Scientific reports

Year

2019

Ovarian carcinoma is caused by multiple factors, but its etiology associated with microbes and infection is unknown. Using 16S rRNA high-throughput sequencing methods, the diversity and composition of the microbiota from ovarian cancer tissues (25 samples) and normal distal fallopian tube tissues (25 samples) were analyzed. High-throughput sequencing showed that the diversity and richness indexes were significantly decreased in ovarian cancer tissues compared to tissues from normal distal fallopian tubes. The ratio of the two phyla for Proteobacteria/Firmicutes was notably increased in ovarian cancer, which revealed that microbial composition change might be associated with the process of ovarian cancer development. In addition, transcriptome-sequencing (RNA-seq) analyses suggested that the transcriptional profiles were statistically different between ovarian carcinoma and normal distal fallopian tubes. Moreover, a set of genes including 84 different inflammation-associated or immune-associated genes, which had been named as the human antibacterial-response genes were also modulated expression. Therefore, we hypothesize that the microbial composition change, as a novel risk factor, may be involving the initiation and progression of ovarian cancer via influencing and regulating the local immune microenvironment of fallopian tubes except for regular pathways.

Experiment 1

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Curated date: 2021/01/10

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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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Ovarian carcinoma

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

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: 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

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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 Control	Links
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

Edit History Delete

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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 Control	Links
Bacillota
Actinomycetota
Acidobacteriota
Fastidiosipila
Lactococcus
Lactococcus piscium

Revision editor(s): WikiWorks, Peace Sandy