Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
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
- Urolithiasis calculus,kidney stone,urinary stones,urolithiasis,Urolithiasis
- 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
- urinary stone disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with urinary stone disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 136
- Group 1 sample size Number of subjects in the case (exposed) group
- 201
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-26
Source: Figure 6
Description: Bubble plot showing the fold change of differentially abundant common rare (B) taxa associated with health disparities (control and USD phenotypes) in stool samples. Selection of taxa is defined using DESeq2 differential abundance analysis with a false discovery rate-corrected p-value <0.05. Taxa are listed as the number of ASVs within the lowest assigned taxonomy as a means to elucidate the most important taxa associated with USD.
Abundance in Group 1: increased abundance in urinary stone disease patients
Revision editor(s): Joju, Iram jamshed, MyleeeA
