Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study/Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, 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
Polycystic ovary syndrome Cystic disease of ovaries,hyperandrogenemia,Multicystic ovaries,multicystic ovaries,Ovarian Degeneration, Sclerocystic,Ovarian Syndrome, Polycystic,Ovarian Syndromes, Polycystic,Ovaries, Sclerocystic,Ovary Syndrome, Polycystic,Ovary, Sclerocystic,PCO - Polycystic ovaries,Pco1,PCOD - Polycystic ovarian disease,PCOS,Pcos,PCOS - Polycystic ovarian syndrome,PCOS1,Polycystic ovarian disease,polycystic ovarian disease,Polycystic ovarian syndrome,Polycystic ovaries,polycystic ovaries,Polycystic ovaries (disorder),polycystic ovary,polycystic ovary syndrome,polycystic ovary syndrome 1,Sclerocystic Ovarian Degeneration,Sclerocystic Ovaries,Sclerocystic Ovary,Sclerocystic Ovary Syndrome,Stein Leventhal Syndrome,Stein-Leventhal synd.,Stein-Leventhal Syndrome,Stein-Leventhal syndrome,Syndrome, Polycystic Ovary,Syndrome, Stein-Leventhal,Polycystic ovary syndrome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
HC - Healthy Controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
NIR-PCOS - NIR(Non-Insulin Resistance)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
NIR-PCOS - PCOS without insulin resistance
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Administration of antibiotics

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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 3

Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.

Abundance in Group 1: increased abundance in NIR-PCOS - NIR(Non-Insulin Resistance)

NCBI Quality ControlLinks
Bacteroidaceae
Bacteroides
Lachnospira
Lachnospiraceae

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 3

Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.

Abundance in Group 1: decreased abundance in NIR-PCOS - NIR(Non-Insulin Resistance)

NCBI Quality ControlLinks
Prevotella
Prevotellaceae

Revision editor(s): WikiWorks, Peace Sandy