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 collection | N = PD patients | N = controls | Criteria for controls | Average disease duration | Exclusion criteria | Additional notes | DNA/RNA | Sequencing method | Sample handling | |
|---|---|---|---|---|---|---|---|---|---|---|
Qian et al. [42] | Shanghai, China | 45 | 45 | Spouses | 5.7 years | All patients on medication | DNA | V3-V4 amplification; Illumina Miseq | Collected at home in the morning, shipped on ice | |
Lin et al. [43] | Taiwan | 80 | 77 | Age and sex-matched | 7.5 years | IBD, antibiotics or prebiotics within past 3 months | DNA | V3-V4 amplification; Illumina Miseq | Samples immediately flash frozen with DNA stabilizer and stored at -80 | |
Bedarf et al. [44] | Bonn, Germany | 31 | 28 | Only male participants, age-matched | Less than one year | Atypical or secondary PD, chronic inflmmatory GI symptoms including chronic constipation, use of laxatives or immunosuppressants within past 3 months | L-DOPA naive | Shotgun sequencing with Illumina Hiseq | ||
Petrov et al. [45] | Moscow, Russia | 89 | 66 | DNA | V3-V4 amplification; Illumina Miseq | |||||
Keshavarzian et al. [39] | Chicago, USA | 38 | 34 | 6.4 years | Atypical 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 | DNA | High-trhoughput amplicon sequencing of V4 | |||
Scheperjans et al. [46] | Helsinki, Finland | 72 | 72 | Age and sex-matched | 5 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. | DNA | Pyrosequencing of V1-V3 regions | Collected at home, stored with DNA stabilizer; frozen at -80 within 3 days | |
Hopfner et al. [47] | Kiel, Germany | 29 | 29 | 11 years | GI comorbidities and antibiotic use within last 3 months | DNA | V1-V2 amplification; Illumina Miseq | Collected at hospital or home, no preservation for up to 48 hours, then stored at -80 | ||
Hasegawa et al. [48] | Nagoya, Japan | 45 | 35 | Spouses | 9,5 years | Atypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness | RNA | RT-qPCR of 16S or 23S rRNA | Collected at hospital, stored with RNA stabilizer, stored at 4C | |
Li et al. [49] | Beijing, China | 24 | 14 | Age and sex-matched | DNA | V3-V5 amplification; Illumina Miseq | Collected at hospital or home, stored at -80C | |||
Aho et al. [44] | Helsinki, Finland | 64 | 64 | Age and sex-matched | 7.5 years (median Scherpejans et al. + 2.5) | Follow-up to Scherpejans et al. Same participants | DNA | V3-V4 amplification; Illumina Miseq | Collected at home, stored with DNA stabilizer; frozen at -80 within 3 days | |
Pereira et al. [41] | Helsinki, Finland | 72, 69 (oral/nasal) | 76, 67 (oral/nasal) | Age and sex-matched | 5 (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. | DNA | V3-V4 amplification; Illumina Miseq | Swabbing of oral and nasal cavities, on ice for 20 mins, stored at -80C | |
Hill-Burns et al. [50] | Seattle, Atlanta, and Albany; USA | 197 | 130 | 54 pairs were spouses; rest unrelated | 13.7 years | DNA | Illumina Miseq | Collected at home, shipped with postal services at ambient temperatures | ||
Unger et al. [51] | Saar, Germany | 34 | 34 | Age-matched | 8 years | Chronic or acute GI diseases, probiotic or antibiotic use within past 3 months | All patients on dopamine medication | DNA | RT-qPCR | Collected at home, sent to center, stored at -35C |
Minato et al. [57] | Nagoya, Japan | 36 | 78 | 11.5 years (2 years after Hasegawa et al.) | Follow-up to Hasegawa et al. | RNA | RT-qPCR of 16S or 23S rRNA | Collected at hospital, stored with RNA stabilizer, stored at 4C | ||
Heintz- Buschart et al. [40] | Helsinki, Finland | 76 | 10 | 7 years | Other neurological symptoms | Only 84 fecal samples were included in final analysis | DNA | V4 amplification; Illumina Hiseq | ||
Li, F et al. [52] | Jinzhou, China | 10 | 72 | 6.2 years | Primary GI disease, alcohol abuse, pancreatic disease, B-hypovitaminosis, infection or antibiotic use within past month, sever gynecological prolapse, regular use of medication | DNA | Pyrosequencing of V1-V3 regions | Samples immediately flash frozen with DNA stabilizer and stored at -80 | ||
Pietrucci et al. [53] | Rome, Italy | 80 | 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 | DNA | V3-V4 amplification; Illumina Miseq | Collected at home, stored with DNA stabilizer stored at ambient temperatures | |||
Lin A et al. [54] | Guangzhou, China | 75 | 45 | Spouses | 4.5 years | Atypical or secondary PD, use of antibiotics or prbiotics within 3 months, primary GI pathology, unstable neurology or psychiatric illness | DNA | V4 amplification; Illumina Hiseq | Samples immediately flash frozen and stored at -80 |