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Table 2 Summary of the techniques and criteria employed by the different microbiome studies of PD patients compared to healthy controls

From: Microbiome changes: an indicator of Parkinson’s disease?

 Country of sample collectionN = PD patientsN = controlsCriteria for controlsAverage disease durationExclusion criteriaAdditional notesDNA/RNASequencing methodSample handling
Qian et al. [42]Shanghai, China4545Spouses5.7 years All patients on medicationDNAV3-V4 amplification; Illumina MiseqCollected at home in the morning, shipped on ice
Lin et al. [43]Taiwan8077Age and sex-matched7.5 yearsIBD, antibiotics or prebiotics within past 3 months DNAV3-V4 amplification; Illumina MiseqSamples immediately flash frozen with DNA stabilizer and stored at -80
Bedarf et al. [44]Bonn, Germany3128Only male participants, age-matchedLess than one yearAtypical or secondary PD, chronic inflmmatory GI symptoms including chronic constipation, use of laxatives or immunosuppressants within past 3 monthsL-DOPA naive Shotgun sequencing with Illumina Hiseq 
Petrov et al. [45]Moscow, Russia8966    DNAV3-V4 amplification; Illumina Miseq 
Keshavarzian et al. [39]Chicago, USA3834 6.4 yearsAtypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness, low platelet count prolonged prothrombin time or history of bleeding DNAHigh-trhoughput amplicon sequencing of V4 
Scheperjans et al. [46]Helsinki, Finland7272Age and sex-matched5 years (median)Motor symptom onset before age 50 and having more than one relative or first-degree relative with PD, smoking, dementia, depression or psychosis, HIV, primary GI disease, endocrinological disease, alcohol abuse, pancreatic disease, bleeding disorders, infections, antibiotic use within last month, etc. DNAPyrosequencing of V1-V3 regionsCollected at home, stored with DNA stabilizer; frozen at -80 within 3 days
Hopfner et al. [47]Kiel, Germany2929 11 yearsGI comorbidities and antibiotic use within last 3 months DNAV1-V2 amplification; Illumina MiseqCollected at hospital or home, no preservation for up to 48 hours, then stored at -80
Hasegawa et al. [48]Nagoya, Japan4535Spouses9,5 yearsAtypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness RNART-qPCR of 16S or 23S rRNACollected at hospital, stored with RNA stabilizer, stored at 4C
Li et al. [49]Beijing, China2414Age and sex-matched   DNAV3-V5 amplification; Illumina MiseqCollected at hospital or home, stored at -80C
Aho et al. [44]Helsinki, Finland6464Age and sex-matched7.5 years (median Scherpejans et al. + 2.5) Follow-up to Scherpejans et al. Same participantsDNAV3-V4 amplification; Illumina MiseqCollected at home, stored with DNA stabilizer; frozen at -80 within 3 days
Pereira et al. [41]Helsinki, Finland72, 69 (oral/nasal)76, 67 (oral/nasal)Age and sex-matched5 (median)Motor symptom onset before age 50 and having more than one relative or first-degree relative with PD, smoking, dementia, depression or psychosis, HIV, primary GI disease, endocrinological disease, alcohol abuse, pancreatic disease, bleeding disorders, infections, antibiotic use within last month, diseases of nose or mouth cavity, etc. DNAV3-V4 amplification; Illumina MiseqSwabbing of oral and nasal cavities, on ice for 20 mins, stored at -80C
Hill-Burns et al. [50]Seattle, Atlanta, and Albany; USA19713054 pairs were spouses; rest unrelated13.7 years  DNAIllumina MiseqCollected at home, shipped with postal services at ambient temperatures
Unger et al. [51]Saar, Germany3434Age-matched8 yearsChronic or acute GI diseases, probiotic or antibiotic use within past 3 monthsAll patients on dopamine medicationDNART-qPCRCollected at home, sent to center, stored at -35C
Minato et al. [57]Nagoya, Japan3678 11.5 years (2 years after Hasegawa et al.) Follow-up to Hasegawa et al.RNART-qPCR of 16S or 23S rRNACollected at hospital, stored with RNA stabilizer, stored at 4C
Heintz- Buschart et al. [40]Helsinki, Finland7610 7 yearsOther neurological symptomsOnly 84 fecal samples were included in final analysisDNAV4 amplification; Illumina Hiseq 
Li, F et al. [52]Jinzhou, China1072 6.2 yearsPrimary GI disease, alcohol abuse, pancreatic disease, B-hypovitaminosis, infection or antibiotic use within past month, sever gynecological prolapse, regular use of medication DNAPyrosequencing of V1-V3 regionsSamples immediately flash frozen with DNA stabilizer and stored at -80
Pietrucci et al. [53]Rome, Italy80 Mostly spouses Atypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness, anamnesis, autoimmune or infectious diseases DNAV3-V4 amplification; Illumina MiseqCollected at home, stored with DNA stabilizer stored at ambient temperatures
Lin A et al. [54]Guangzhou, China7545Spouses4.5 yearsAtypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness DNAV4 amplification; Illumina HiseqSamples immediately flash frozen and stored at -80
  1. All studies used the 16S rRNA gene for sequencing unless otherwise stated