Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR, Askarova S
Journal
Scientific reports
Year
2022
We have investigated the diversity and composition of gut microbiotas isolated from AD (Alzheimer's disease) patients (n = 41) and healthy seniors (n = 43) from Nur-Sultan city (Kazakhstan). The composition of the gut microbiota was characterized by 16S ribosomal RNA sequencing. Our results demonstrated significant differences in bacterial abundance at phylum, class, order, and genus levels in AD patients compared to healthy aged individuals. Relative abundance analysis has revealed increased amount of taxa belonging to Acidobacteriota, Verrucomicrobiota, Planctomycetota and Synergistota phyla in AD patients. Among bacterial genera, microbiotas of AD participants were characterized by a decreased amount of Bifidobacterium, Clostridia bacterium, Castellaniella, Erysipelotrichaceae UCG-003, Roseburia, Tuzzerella, Lactobacillaceae and Monoglobus. Differential abundance analysis determined enriched genera of Christensenellaceae R-7 group, Prevotella, Alloprevotella, Eubacterium coprostanoligenes group, Ruminococcus, Flavobacterium, Ohtaekwangia, Akkermansia, Bacteroides sp. Marseille-P3166 in AD patients, whereas Levilactobacillus, Lactiplantibacillus, Tyzzerella, Eubacterium siraeum group, Monoglobus, Bacteroides, Erysipelotrichaceae UCG-003, Veillonella, Faecalibacterium, Roseburia, Haemophilus were depleted. We have also found correlations between some bacteria taxa and blood serum biochemical parameters. Adiponectin was correlated with Acidimicrobiia, Faecalibacterium, Actinobacteria, Oscillospiraceae, Prevotella and Christensenellaceae R-7. The Christensenellaceae R-7 group and Acidobacteriota were correlated with total bilirubin, while Firmicutes, Acidobacteriales bacterium, Castellaniella alcaligenes, Lachnospiraceae, Christensenellaceae and Klebsiella pneumoniae were correlated with the level of CRP in the blood of AD patients. In addition, we report the correlations found between disease severity and certain fecal bacteria. This is the first reported study demonstrating gut microbiota alterations in AD in the Central Asian region.

Experiment 1


Needs review

Curated date: 2024/03/13

Curator: EniolaAde

Revision editor(s): EniolaAde

Subjects

Location of subjects
Kazakhstan
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
Healthy senior group
Group 1 name Corresponds to the case (exposed) group for case-control studies
Alzheimer's group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients with Alzheimer's disease
Group 0 sample size Number of subjects in the control (unexposed) group
43
Group 1 sample size Number of subjects in the case (exposed) group
41

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
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
ANOSIM
PERMANOVA
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)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/03/13

Curator: EniolaAde

Revision editor(s): EniolaAde

Source: Figure 2 and Supplementary file Table 1a,b,c

Description: violin plots of deferentially abundant taxa between healthy control group and Alzheimer's disease group

Abundance in Group 1: increased abundance in Alzheimer's group

NCBI Quality ControlLinks
Akkermansia
Cloacibacillus
Corynebacterium
Eubacterium
Flavobacterium
Longimicrobium
Niastella
Oxalobacter
Parasegetibacter
Polaromonas
Prevotella
Solitalea
Vicinamibacter
metagenome
Acidobacteriota
Candidatus Latescibacterota
Planctomycetota
Synergistota
Verrucomicrobiota
Blastocatellia
Acidimicrobiia
incerta sedisincerta sedis
Phycisphaerae
pla4 lineagepla4 lineage
Synergistia
Verrucomicrobiae
uncultured soil bacterium
utbcd1utbcd1
mm2mm2
miz17miz17
Dinghuibacter
Thioalkalivibrio
Methylotenera
Candidatus Udaeobacter

Revision editor(s): EniolaAde

Signature 2

Needs review

Curated date: 2024/03/13

Curator: EniolaAde

Revision editor(s): EniolaAde

Source: Figure 2 and Supplementary file Table 1 a,b,c

Description: violin plots of deferentially abundant taxa between healthy control group and Alzheimer's disease group

Abundance in Group 1: decreased abundance in Alzheimer's group

NCBI Quality ControlLinks
Bifidobacterium
Castellaniella
Haemophilus
Lactiplantibacillus
Latilactobacillus
Levilactobacillus
Monoglobus
Phyllobacterium
Roseburia
Tyzzerella
Veillonella
gut metagenome
uncultured Clostridia bacterium
erysipelotrichaceae ucg-003erysipelotrichaceae ucg-003
Actinomycetota
lachnospiraceae ucg-001lachnospiraceae ucg-001
Nitrosococcus

Revision editor(s): EniolaAde

Experiment 2


Needs review

Curated date: 2024/03/13

Curator: EniolaAde

Revision editor(s): EniolaAde

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Alzheimer's disease group

Lab analysis

Statistical Analysis

Statistical test
LEfSe
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/03/18

Curator: EniolaAde

Revision editor(s): EniolaAde, Ayibatari

Source: Figure 3c

Description: LEfSe differential abundant taxa between healthy senior groups and patients with Alzheimer's disease group

Abundance in Group 1: increased abundance in Alzheimer's disease group

NCBI Quality ControlLinks
Acidimicrobiia
Acidobacteriota
Akkermansia muciniphila
Alloprevotella
Bacillota
Bacteria
Bacteroides
Bifidobacterium
Christensenellaceae
Clostridia
Dialister
Eubacterium coprostanoligenes
Oscillospiraceae
Ruminococcus
Sutterella
gut metagenome
uncultured Bacteroidetes bacterium
uncultured organism
uncultured soil bacterium
clostridia ucg-014clostridia ucg-014
uncultured acidobacteriales bacteriumuncultured acidobacteriales bacterium
marseille-P3166marseille-P3166
Hyphomicrobiales

Revision editor(s): EniolaAde, Ayibatari

Signature 2

Needs review

Curated date: 2024/03/19

Curator: EniolaAde

Revision editor(s): EniolaAde

Source: Figure 3c

Description: LEfSe differential abundant taxa between healthy senior groups and patients with Alzheimer's disease group

Abundance in Group 1: decreased abundance in Alzheimer's disease group

NCBI Quality ControlLinks
Levilactobacillus
Bacteroidales
Gammaproteobacteria
Tyzzerella
Eubacterium
Monoglobus
Bacteroides
Veillonella
Clostridia
Alcaligenes sp. ES-JQ-2
erysipelotrichaceae ucg-003erysipelotrichaceae ucg-003
Faecalibacterium
Lactiplantibacillus plantarum
Bacilli
Haemophilus
uncultured organism
Enterobacterales
Lachnospirales
Actinomycetota
gut metagenome
Lachnospiraceae
Bacillota

Revision editor(s): EniolaAde