Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression/Experiment 5

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

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: Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Tremor-dominant phenotype (TD) at follow-up

Group 1 name Corresponds to the case (exposed) group for case-control studies: Postural instability and gait difficulty (PIGD) phenotype at follow-up

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Parkinson's disease patients with PIGD phenotype at follow-up

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): none

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

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

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Peace Sandy, ChiomaBlessing, Folakunmi, Hodan Issah

Source: Table S8 (B) in supplementary results.

Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at follow-up

Abundance in Group 1: decreased abundance in Postural instability and gait difficulty (PIGD) phenotype at follow-up

NCBI	Quality Control	Links
Barnesiella
Lactococcus
unclassified Clostridiaceae
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Porphyromonadaceae
Clostridium XIVaClostridium XIVa
Anaeroplasmataceae
Asteroleplasma
unclassified Eubacteriales
unclassified Clostridia