External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Lee CC, Liang F, Lee IC, Lu TH, Shan YY, Jeng CF, Zou YF, Yu HT, Chen Alen SK
Journal
EMBO reports
Year
2022
Keywords:
dim light at night, gut microbiota, ipRGC, melanopsin
Gut microbiota are involved in many physiological functions such as metabolism, brain development, and neurodegenerative diseases. Many microbes in the digestive tract do not maintain a constant level of their relative abundance but show daily oscillations under normal conditions. Recent evidence indicates that chronic jetlag, constant darkness, or deletion of the circadian core gene can alter the composition of gut microbiota and dampen the daily oscillation of gut microbes. However, the neuronal circuit responsible for modulating gut microbiota remained unclear. Using genetic mouse models and 16s rRNA metagenomic analysis, we find that light-dark cycle information transmitted by the intrinsically photosensitive retinal ganglion cells (ipRGCs) is essential for daily oscillations of gut microbes under temporal restricted high-fat diet conditions. Furthermore, aberrant light exposure such as dim light at night (dLAN) can alter the composition, relative abundance, and daily oscillations of gut microbiota. Together, our results indicate that external light-dark cycle information can modulate gut microbiota in the direction from the brain to the gut via the sensory system.
Experiment 1
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) - 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
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
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
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
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
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-9-24
Differences from previous experiment shown
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
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
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