39940045/Experiment 9: Difference between revisions
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KateRasheed (talk | contribs) (Created page with "{{Experiment |Base page=39940045 |Host species=Not specified |Group 0 name=Fiber intake Strata before Pasteurized Sauerkraut Intervention: Fiber ≥ 30g (30-58g) |Group 1 name=Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g) |Group 1 definition=Participants with ≥ 30g (30-58g) fiber diet that received fresh Sauerkraut Intervention. |Antibiotics exclusion=3 months |Sequencing type=WMS |Sequencing platform=Illumina |Data transformation=rela...") |
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{{Experiment | {{Experiment | ||
|Base page=39940045 | |Base page=39940045 | ||
|Host species= | |Location of subjects=Germany | ||
|Host species=Homo sapiens | |||
|Body site=Feces | |||
|Condition=Diet | |||
|Group 0 name=Fiber intake Strata before Pasteurized Sauerkraut Intervention: Fiber ≥ 30g (30-58g) | |Group 0 name=Fiber intake Strata before Pasteurized Sauerkraut Intervention: Fiber ≥ 30g (30-58g) | ||
|Group 1 name=Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g) | |Group 1 name=Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g) | ||
| Line 17: | Line 20: | ||
|Inverse Simpson=unchanged | |Inverse Simpson=unchanged | ||
|Richness=unchanged | |Richness=unchanged | ||
|State= | |State=Complete | ||
}} | }} | ||
Revision as of 16:20, 24 March 2025
Reviewed Marked as Reviewed by Svetlana up on 2025-3-25
Subjects
- Location of subjects
- Germany
- 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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Fiber intake Strata before Pasteurized Sauerkraut Intervention: Fiber ≥ 30g (30-58g)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with ≥ 30g (30-58g) fiber diet that received fresh Sauerkraut Intervention.
- 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
- 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
- Mixed-Effects Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "fibre intake" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.fibre intake
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-25
Source: Supplementary Figure 11
Description: Species’ relative abundance before fresh intervention vs after fresh intervention
Abundance in Group 1: increased abundance in Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g)
| NCBI | Quality Control | Links |
|---|---|---|
| Lacticaseibacillus paracasei |
Revision editor(s): KateRasheed
