Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel/Experiment 3

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
LD (Levodopa)
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
46
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
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

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 3C

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

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

NCBI Quality ControlLinks
Aeromonadaceae
Bacteroides rodentium
Butyricimonas
Desulfovibrio
Dethiosulfovibrionaceae
Enterobacter
Enterobacter soli
Enterobacteriaceae
Erwinia
Erwiniaceae
Escherichia
Klebsiella
Klebsiella granulomatis
Klebsiella variicola
Odoribacter
Odoribacteraceae
Oscillospiraceae
Parabacteroides
Phascolarctobacterium faecium
Pseudomonadota
Serratia
Serratia entomophila
Sphingobacteriaceae
Tolumonas
Tolumonas auensis
Anaerotruncus
Parabacteroides johnsonii
Eubacterium
Lactobacillus taiwanensis
Phocaeicola sartorii
Desulfovibrio piger
Sutterella sanguinus
Desulfotomaculum
Phocaeicola paurosaccharolyticus
Anaerofilum

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 3C

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

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

NCBI Quality ControlLinks
Tindallia
Sedimentibacter
Peptostreptococcaceae
Blautia hansenii
Lachnospira
Lactobacillus
Lactobacillaceae
Clostridiaceae
Bacillota

Revision editor(s): Anne-mariesharp