Study 1067

Study information

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• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
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Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s12866-020-01918-0

URI

Authors

Journal

Year

Experiment 1

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Needs review

Curated date: 2024/03/25

Curator: Ndruscilla

Revision editor(s): Ndruscilla

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

Vaginal fluid , Blood Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid,Portion of blood,Vertebrate blood,Whole blood,Blood,blood

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

Acquired primary ovarian failure acquired premature ovarian failure,acquired primary ovarian failure,Acquired primary ovarian failure

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

POF

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

women with POF

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

29

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

22

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

3 months prior to enrolment

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

Random Forest Analysis

Spearman Correlation

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

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

2

Matched on Factors on which subjects have been matched on in a case-control study

smoking behavior, chronic kidney disease, accute-on-chronic liver failure, age

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

increased

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

increased

Richness Number of species

increased

Signature 1

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Mark reviewed

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Needs review

Curated date: 2024/03/25

Curator: Ndruscilla

Revision editor(s): Ndruscilla

Source: Figure 2

Description: Abundance of different taxa using LEfSe analysis

Abundance in Group 1: increased abundance in POF

NCBI	Quality Control	Links
Gardnerella
Prevotella
Bacteroides
Sneathia
Dialister
Anaerococcus

Revision editor(s): Ndruscilla

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/03/25

Curator: Ndruscilla

Revision editor(s): Ndruscilla

Source: Figure 2

Description: Abundance of different taxa using LEfSe analysis

Abundance in Group 1: decreased abundance in POF

NCBI	Quality Control	Links
Lactobacillus

Revision editor(s): Ndruscilla