Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls
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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.
URI Uniform resource identifier for web resources.
Authors
Teigen LM, McCarter SJ, Ziegert Z, Staley C, Grant KM, Gupta VK, Zhao X, St Louis EK, Kantarci K, Lowe VJ, Forsberg LK, Savica R, Ramanan VK, Jones DT, Petersen RC, Sung J, Khoruts A, Boeve BF, Ross OA
Journal
Parkinsonism & related disorders
Year
2024
BACKGROUND: Microbial dysbiosis has been reported to contribute to development of neurodegenerative diseases, however, there is a need to identify causative/prognostic indicators. OBJECTIVES: To comparatively analyze gut microbiome composition in symptomatic LBD (dementia/mild cognitive impairment), iRBD, and cohabiting controls without LBD or iRBD. METHODS: 16S rRNA amplicon sequencing was performed in 38 cases (27 LBD, 11 iRBD) and 39 cohabitant controls. 19 non-cohabitant healthy controls (HCs) were also included to contrast differences between cohabitant cases and controls. RESULTS: Microbiome composition of cohabitant controls and LBD and iRBD cases were strikingly similar. No differences were observed between LBD, and iRBD only showed reduced Bacteroides, compared with cohabitant controls. There were several taxonomic differences in gut microbiome composition between non-cohabitant HCs and cases. CONCLUSIONS: Minimal microbiome differences were observed between iRBD or LBD cases and cohabitant controls. These findings underscore the importance of using cohabiting controls in future gut microbiome studies.
Experiment 1
Needs review
Subjects
- Location of subjects
- United States of America
- 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
- REM sleep behavior disorder Rapid eye movement sleep behavior disorder,rapid eye movement sleep behavior disorder,REM Sleep Behavior Disorder,REM sleep behavior disorder,rEM sleep behavior disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cohabitant controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cases with iRBD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- isolated REM sleep behavior disorder (iRBD) cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0083
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 1
Description: Taxa depleted in iRBD cases.
Abundance in Group 1: decreased abundance in cases with iRBD
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Kristin.abraham
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lewy body dementia dementia with Lewy bodies,dementia, Lewy body,diffuse Lewy body disease,diffuse Lewy body disease with gaze palsy,DLB,Lewy body dementia,Lewy body disease,Lewy body variant of Alzheimer disease,Senile dementia of the Lewy body type,lewy body dementia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LBD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Lewy Body Dementia (LBD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Figure 1
Description: Taxa enriched in LBD patients.
Abundance in Group 1: increased abundance in LBD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia |
Revision editor(s): Kristin.abraham
Signature 2
Needs review
Source: Figure 1
Description: Taxa depleted in LBD patients.
Abundance in Group 1: decreased abundance in LBD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Faecalibacterium | ||
| Lachnospiraceae |
Revision editor(s): Kristin.abraham
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- REM sleep behavior disorder Rapid eye movement sleep behavior disorder,rapid eye movement sleep behavior disorder,REM Sleep Behavior Disorder,REM sleep behavior disorder,rEM sleep behavior disorder
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- iRBD cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- isolated REM sleep behavior disorder (iRBD) cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 1
Description: Taxa enriched in iRBD cases
Abundance in Group 1: increased abundance in iRBD cases
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia |
Revision editor(s): Kristin.abraham
Signature 2
Needs review
Source: Figure 1
Description: Taxa depleted in iRBD cases
Abundance in Group 1: decreased abundance in iRBD cases
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides |
Revision editor(s): Kristin.abraham
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lewy body dementia , REM sleep behavior disorder dementia with Lewy bodies,dementia, Lewy body,diffuse Lewy body disease,diffuse Lewy body disease with gaze palsy,DLB,Lewy body dementia,Lewy body disease,Lewy body variant of Alzheimer disease,Senile dementia of the Lewy body type,lewy body dementia,Rapid eye movement sleep behavior disorder,rapid eye movement sleep behavior disorder,REM Sleep Behavior Disorder,REM sleep behavior disorder,rEM sleep behavior disorder
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cohabitant controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cohabitants of Lewy Body Dementia (LBD) and isolated REM Sleep Behavior Disorder (iRBD) cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Figure 1
Description: Taxa enriched in cohabitant controls
Abundance in Group 1: increased abundance in Cohabitant controls
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia |
Revision editor(s): Kristin.abraham
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