Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel/Experiment 2

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
LCIG (Levodopa-carbidopa intestinal gel)
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-carbidopa intestinal gel
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
38
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 3B

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

Abundance in Group 1: increased abundance in LCIG (Levodopa-carbidopa intestinal gel)

NCBI Quality ControlLinks
Butyricimonas
Collinsella
Desulfovibrio
Enterobacter soli
Erysipelothrix muris
Lactobacillus taiwanensis
Serratia entomophila
Tolumonas
Aeromonadaceae
Serratia
Klebsiella variicola
Klebsiella granulomatis
Lactobacillus
Lactobacillaceae
Enterobacter
Erwinia
Klebsiella
Enterococcus
Escherichia
Enterobacteriaceae
Pseudomonadota

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 3B

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

Abundance in Group 1: decreased abundance in LCIG (Levodopa-carbidopa intestinal gel)

NCBI Quality ControlLinks
Actinomyces
Actinomycetaceae
Bacillota
Bifidobacterium scardovii
Blautia
Blautia hansenii
Blautia wexlerae
Clostridiaceae
Clostridium thermosuccinogenes
Coprococcus
Desulfovibrio piger
Dorea
Erysipelothrix
Erysipelotrichaceae
Faecalibacterium
Faecalibacterium prausnitzii
Kitasatospora
Lachnospira
Lachnospira pectinoschiza
Lachnospiraceae
Natronincola
Oscillospira guilliermondii
Oscillospiraceae
Peptococcaceae
Pseudobutyrivibrio
Pseudobutyrivibrio xylanivorans
Roseburia
Roseburia faecis
Ruminococcus bromii
Schaalia naturae
Sedimentibacter
Streptomycetaceae
Thiothrix
Thiotrichaceae
Tindallia

Revision editor(s): Anne-mariesharp