Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Subjects
- 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
- Male homosexuality Male homosexuality,male homosexuality
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Men with 0-3 sexual partners
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Men with >3 sexual partners
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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).
- 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
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Source: figure 4 (c) and Supplementary Table S4
Description: Species-level taxonomic biomarkers identified using LEfSe to associate with behaviors having >3 (and 0–3) sexual partners.
Abundance in Group 1: decreased abundance in Men with >3 sexual partners
Revision editor(s): Uhabiba14, Fiddyhamma, MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Source: figure 4C and SupplementaryTable S4
Description: Species-level taxonomic biomarkers identified using LEfSe58 to associate with behaviors having ( 0–3) sexual partners. Only taxonomically known species are displayed
Abundance in Group 1: increased abundance in Men with >3 sexual partners
Revision editor(s): Uhabiba14, MyleeeA, Fiddyhamma
