External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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) - Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dim light at night (dLAN) - Control 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 control group
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
- increased
Signature 1
Source: Figure 4B
Description: Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.
Abundance in Group 1: increased abundance in Dim light at night (dLAN) - Control group
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Paraprevotella | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Enterococcaceae bacterium RF39 |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4B
Description: Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.
Abundance in Group 1: decreased abundance in Dim light at night (dLAN) - Control group
| NCBI | Quality Control | Links |
|---|---|---|
| Rikenella | ||
| Odoribacter | ||
| Odoribacteraceae |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal light‐dark cycle (LD) - MKO group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dim light at night (dLAN) - MKO 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 with knockout of the photopigment melanopsin (MKO).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 3
Subjects
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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
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
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal light‐dark cycle (LD) - Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal light‐dark cycle (LD) - MKO group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exposure to normal daily light‐dark cycle (LD) in the group with knockout of the photopigment melanopsin (MKO).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4B and 4C
Description: Figure 4B and 4C represents a cladogram that shows the difference in the relative abundance of microbes from control mice and MKO mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: decreased abundance in Normal light‐dark cycle (LD) - MKO group
| NCBI | Quality Control | Links |
|---|---|---|
| Odoribacter | ||
| Odoribacteraceae | ||
| Rikenella |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal light‐dark cycle (LD) - DTA group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exposure to normal daily light‐dark cycle (LD) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4B and 4D
Description: Figure 4B and 4D represents a cladogram that shows the difference in the relative abundance of microbes from control mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: increased abundance in Normal light‐dark cycle (LD) - 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
Signature 2
Source: Figure 4B and 4D
Description: Figure 4B and 4D represents a cladogram that shows the difference in the relative abundance of microbes from control mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: decreased abundance in Normal light‐dark cycle (LD) - DTA group
| NCBI | Quality Control | Links |
|---|---|---|
| Rikenella | ||
| Odoribacter | ||
| Odoribacteraceae |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Dim light at night (dLAN) - Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dim light at night (dLAN) - MKO 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 with knockout of the photopigment melanopsin (MKO).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4B and 4C
Description: Figure 4B and 4C represents a cladogram that shows the difference in the relative abundance of microbes from control mice and MKO mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: decreased abundance in Dim light at night (dLAN) - MKO group
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Paraprevotella | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Enterococcaceae bacterium RF39 |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4B and 4D
Description: Figure 4B and 4D represents a cladogram that shows the difference in the relative abundance of microbes from control mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
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
Source: Figure 4B and 4D
Description: Figure 4B and 4D represents a cladogram that shows the difference in the relative abundance of microbes from control mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: decreased abundance in Dim light at night (dLAN) - DTA group
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Paraprevotella | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Enterococcaceae bacterium RF39 |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal light‐dark cycle (LD) - MKO group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal light‐dark cycle (LD) - DTA group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exposure to normal daily light‐dark cycle (LD) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4C and 4D
Description: Figure 4C and 4D represents a cladogram that shows the difference in the relative abundance of microbes from MKO mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
Abundance in Group 1: increased abundance in Normal light‐dark cycle (LD) - DTA group
| NCBI | Quality Control | Links |
|---|---|---|
| bacterium AF12 | ||
| Rikenellaceae | ||
| rumen bacterium YS2 | ||
| Enterococcaceae bacterium RF39 | ||
| bacterium F16 | ||
| TM7 phylum sp. oral clone CW040 |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Dim light at night (dLAN) - MKO 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 4C and 4D
Description: Figure 4C and 4D represents a cladogram that shows the difference in the relative abundance of microbes from MKO mice and DTA mice housed under conditions of Normal light‐dark cycle (LD) and Dim light at night (dLAN).
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
