Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-4-29

Curated date: 2025/04/12

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Subjects

Location of subjects
Italy
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
Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Naive
Group 1 name Corresponds to the case (exposed) group for case-control studies
LD (Levodopa)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Parkinson’s Disease patients treated with levodopa
Group 0 sample size Number of subjects in the control (unexposed) group
23
Group 1 sample size Number of subjects in the case (exposed) group
46
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-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
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-4-29

Curated date: 2025/04/12

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3A

Description: LEfSE comparison between LD and Naive groups showing significantly enriched taxa

Abundance in Group 1: increased abundance in LD (Levodopa)

NCBI Quality ControlLinks
Erysipelothrix muris
Collinsella
Collinsella aerofaciens

Revision editor(s): Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-4-29

Curated date: 2025/04/12

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3A

Description: LEfSE comparison between LD and Naive groups showing significantly enriched taxa

Abundance in Group 1: decreased abundance in LD (Levodopa)

NCBI Quality ControlLinks
Bacteroides rodentium
Bacteroides stercoris
Blautia wexlerae
Erysipelothrix
Erysipelotrichaceae
Faecalibacterium
Faecalibacterium prausnitzii
Oscillospiraceae
Pseudobutyrivibrio
Pseudobutyrivibrio xylanivorans
Roseburia
Ruminococcus bromii
Eubacterium
Dorea
Phascolarctobacterium faecium
Lachnospira pectinoschiza
Natronincola
Parabacteroides johnsonii
Clostridium thermosuccinogenes
Actinomyces
Odoribacter
Anaerofilum
Actinomycetaceae
Phocaeicola sartorii
Schaalia naturae
Thiotrichaceae
Thiothrix
Bifidobacterium scardovii
Bifidobacterium
Johnsonella ignava
Desulfotomaculum
Phocaeicola paurosaccharolyticus
Streptomycetaceae
Sutterella sanguinus
Oscillospira guilliermondii
Dethiosulfovibrionaceae
Kitasatospora
Tolumonas
Aeromonadaceae
Tolumonas auensis

Revision editor(s): Anne-mariesharp