Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study
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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
Lwere K, Muwonge H, Sendagire H, Sajatovic M, Williams SM, Gumukiriza-Onoria JL, Buwembo D, Buwembo W, Nassanga R, Nakimbugwe R, Nazziwa A, Munabi IG, Nakasujja N, Kaddumukasa M
Journal
Medicine
Year
2025
Keywords:
Alzheimer disease, gut microbiome, mild cognitive impairment
Alzheimer disease (AD) is associated with significant shifts in the gut microbiome and is characterized by reduced microbial diversity and changes in the abundance of specific taxa. These alterations can disrupt the gut-brain axis, leading to increased intestinal permeability ("leaky gut"), systemic inflammation, and oxidative stress. Such microbial changes are thought to contribute to neurodegenerative changes, as observed in AD and cognitive decline, thus emphasizing the role of the microbiome in aging-related neurological health. Our study in urban and rural population in Uganda recruited 104 participants aged 60 years and older, categorized into AD, mild cognitive impairment (MCI), and control groups based on Montreal Cognitive Assessment (MoCA) scores and ICD-11/DSM-V criteria. DNA was extracted from fecal samples using a QIAamp kit and polymerase chain reaction (PCR) products were sequenced using Nanopore. We used diversity indices, principal coordinate analysis (PCoA), permutational multivariate analysis of variance (PERMANOVA), and linear discriminant analysis effect size (LefSe) to identify significant microbial differences among groups. Gut microbiome diversity, as measured by the Chao1 and Shannon indices, was significantly reduced in patients with AD. The AD group had the lowest diversity compared to that of the control group (P < .05). PCoA showed distinct microbial shifts between patients with AD and controls, with MCI showing an intermediate profile. Genera such as Novosphingobium and Staphylococcus were more prevalent in the controls, whereas Hafnia-Obesumbacterium and Dickeya were more common in AD. Age-related changes included increases in Exiguobacterium and Carnobacterium and decreases in Acinetobacter and Klebsiella. Distinct microbial profiles were identified in the AD, MCI, and control groups, suggesting potential microbiome markers of cognitive impairment in the Ugandan population.
Experiment 1
Needs review
Subjects
- Location of subjects
- Uganda
- 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
- Alzheimer's disease [X]Dementia in Alzheimer's disease,[X]Dementia in Alzheimer's disease (disorder),AD,AD - Alzheimer's disease,Alzheimer Dementia,Alzheimer dementia,Alzheimer Dementia, Presenile,ALZHEIMER DIS,Alzheimer Disease,Alzheimer disease,Alzheimer disease, familial,Alzheimer Type Dementia,Alzheimer's,Alzheimer's Dementia,Alzheimer's dementia,Alzheimer's disease,Alzheimer's disease (disorder),Alzheimer's disease, NOS,Alzheimers,Alzheimers Dementia,Alzheimers dementia,ALZHEIMERS DIS,Alzheimers disease,DAT - Dementia Alzheimer's type,Dementia in Alzheimer's disease,Dementia in Alzheimer's disease (disorder),Dementia in Alzheimer's disease, unspecified (disorder),Dementia of the Alzheimer's type,Dementia, Alzheimer Type,Dementia, Presenile,Dementia, Presenile Alzheimer,Disease, Alzheimer,Disease, Alzheimer's,Presenile Alzheimer Dementia,sporadic Alzheimer's disease,alzheimer's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cognitively healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Alzheimer's Disease (AD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes, excluded participants with recent antibiotic use within 6 weeks
Lab analysis
- Sequencing type
- 16S
- 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
- Nanopore
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Figure 9
Description: Taxa enriched in Alzheimer’s disease patients.
Abundance in Group 1: increased abundance in AD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Cronobacter | ||
| Dickeya | ||
| Hafnia | ||
| Raoultella | ||
| Thermomonas |
Revision editor(s): Kristin.abraham
Signature 2
Needs review
Source: Figure 9
Description: Taxa depleted in Alzheimer’s disease patients.
Abundance in Group 1: decreased abundance in AD patients
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
- Cognitive impairment Abnormality of cognition,Cognitive abnormality,Cognitive defects,Cognitive deficits,Cognitive impairment,Intellectual impairment,cognitive impairment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MCI cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with Mild Cognitive Impairment (MCI)
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes, excluded participants with recent antibiotic use within 6 weeks.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Figure 8
Description: Taxa enriched in MCI cases.
Abundance in Group 1: increased abundance in MCI cases
| NCBI | Quality Control | Links |
|---|---|---|
| Hafnia |
Revision editor(s): Kristin.abraham
Signature 2
Needs review
Source: Figure 8
Description: Taxa depleted in MCI cases.
Abundance in Group 1: decreased abundance in MCI cases
Revision editor(s): Kristin.abraham
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