External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
Subjects
- Location of subjects
- Taiwan
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Light Light,light
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal light‐dark cycle (LD) - DTA group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dim light at night (dLAN) - DTA group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exposure to aberrant light conditions such as dim light at night (dLAN) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
Source: Figure 4D
Description: The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.
Abundance in Group 1: increased abundance in Dim light at night (dLAN) - DTA group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Allobaculum | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Akkermansia | ||
| Verrucomicrobiaceae | ||
| Verrucomicrobiales |
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
Source: Figure 4D
Description: The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.
Abundance in Group 1: decreased abundance in Dim light at night (dLAN) - DTA group
| NCBI | Quality Control | Links |
|---|---|---|
| rumen bacterium YS2 | ||
| Rikenellaceae | ||
| bacterium AF12 | ||
| Enterococcaceae bacterium RF39 | ||
| bacterium F16 | ||
| TM7 phylum sp. oral clone CW040 |
Revision editor(s): Aleru Divine
