Table 3.
Methodological characteristics of included studies (n = 14).
| Characteristics | n (%) | |
|---|---|---|
| Sample | Fecal | 14 (100.0) |
| Immediate storage temperature | 4 °C | 1 (8.3) |
| −20 °C | 6 (50.0) | |
| −80 °C | 5 (41.7) | |
| DNA isolation methods | QIAamp DNA Stool Mini Kit | 8 (61.5) |
| PSP Spin Stool DNA Plus Kit | 1 (7.7) | |
| NucleoSpin Soil kit (Macherey-Nagel | 1 (7.7) | |
| RNeasy Power Microbiome KIT | 1 (7.7) | |
| PowerMax (stool/soil) DNA isolation kit | 1 (7.7) | |
| GTX stool extraction kit | 1 (7.7) | |
| Sequencing | Amplicon | 12 (85.7) |
| Metagenomic | 2 (14.3) | |
| Variable region amplified | V1–V2 | 2 (18.1) |
| V3–V4 | 5 (45.5) | |
| V4 | 3 (27.3) | |
| V6–V8 | 1 (9.1) | |
| Platform | Illumina HiSeq | 5 (45.5) |
| Illumina MiSeq | 8 (61.5) | |
| Unknown | 1 (9.1) | |
| Bioinformatics pipeline | RDP classifier | 1 (7.14) |
| QIIME | 8 (57.1) | |
| MOCAT | 1 (7.14) | |
| Multiple | 4 (28.6) | |
| Reference database | Silva | 6 (50.0) |
| Greengenes | 4 (33.0) | |
| Vsearch | 1 (8.3) | |
| EzTaxon | 1 (8.3) |