Table 4.
Reproducibility of NGS of the 16S-23S region.
| Sample (Growth CFU/ml) | Identification | Detection Frequency (n) | Average (% reads) | Range (% reads)B | SDB |
|---|---|---|---|---|---|
| UR12 (103) | Proteus mirabilis | 3 | 90.0 | 75.5–97.9 | 12.6 |
| Proteus vulgaris | 3 | 6.8 | 0.6–17.5 | 9.3 | |
| Aerococcus urinae | 3 | 1.3 | 1.1–1.5 | 0.2 | |
| Undibacterium oligocarboniphilum A | 1 | 4.8 | n.a. | n.a. | |
| Corynebacterium striatum | 1 | 0.3 | n.a. | n.a. | |
| Pseudomonas saccharophila | 1 | 0.3 | n.a. | n.a. | |
| Enterococcus faecalis | 1 | 0.2 | n.a. | n.a. | |
| Ralstonia pickettii A | 1 | 0.1 | n.a. | n.a. | |
| UR14 (102) | Unidentified species | 3 | 23.6 | 5.3–42.0 | 18.4 |
| Peptoniphilus lacrimalis | 3 | 17.9 | 5.9–33.7 | 14.3 | |
| Fenollaria massiliensis | 3 | 13.5 | 11.6–15.6 | 2.0 | |
| Peptostreptococcus anaerobius | 3 | 9.5 | 4.4–13.1 | 4.5 | |
| Mobiluncus curtisii | 3 | 6.0 | 2.1–10.6 | 4.3 | |
| Anaerococcus sp. | 3 | 3.6 | 1.8–6.6 | 2.6 | |
| Atopobium deltae | 3 | 2.8 | 2.3–3.7 | 0.8 | |
| Dialister propionicifaciens | 3 | 0.8 | 0.6–1.2 | 0.3 | |
| Jonquetella anthropi | 3 | 0.6 | 0.3–1.1 | 0.4 | |
| Tissierella sp. | 2 | 2.3 | 2.0–2.6 | 0.4 | |
| Moryella sp. | 2 | 0.8 | 0.1–1.4 | 0.9 | |
| Fusobacterium nucleatum | 2 | 0.5 | 0.3–0.7 | 0.3 | |
| Ezakiella sp. | 2 | 0.2 | 0.1–0.2 | 0.1 | |
| Undibacterium oligocarboniphilum A | 1 | 36.4 | n.a. | n.a. | |
| Peptoniphilus koenoeneniae | 1 | 4.1 | n.a. | n.a. | |
| Prevotella bivia | 1 | 3.4 | n.a. | n.a. | |
| Pseudomonas saccharophila | 1 | 3.1 | n.a. | n.a. | |
| Candidatus Peptoniphilus massiliensis | 1 | 2.6 | n.a. | n.a. | |
| Peptoniphilus harei | 1 | 1.1 | n.a. | n.a. | |
| Streptococcus anginosus | 1 | 0.8 | n.a. | n.a. | |
| Ralstonia pickettii A | 1 | 0.7 | n.a. | n.a. | |
| Methylobacterium oryzae A | 1 | 0.6 | n.a. | n.a. | |
| Streptococcus sp. | 1 | 0.6 | n.a. | n.a. | |
| Asinibacterium lactis | 1 | 0.5 | n.a. | n.a. | |
| Olsenella sp. | 1 | 0.5 | n.a. | n.a. | |
| Methylobacterium jeotgali A | 1 | 0.4 | n.a. | n.a. | |
| Peptoniphilus duerdenii | 1 | 0.4 | n.a. | n.a. | |
| Filifactor sp. | 1 | 0.2 | n.a. | n.a. | |
| Proteus mirabilis | 1 | 0.2 | n.a. | n.a. | |
| Actinotignum sp. | 1 | 0.2 | n.a. | n.a. | |
| Bacteroides sp. | 1 | 0.2 | n.a. | n.a. | |
| Shigella flexneri | 1 | 0.1 | n.a. | n.a. | |
| Casaltella sp. | 1 | 0.1 | n.a. | n.a. | |
| Howardella sp. | 1 | 0.1 | n.a. | n.a. | |
| Propionibacterium acnes | 1 | 0.1 | n.a. | n.a. | |
| UR22 (102) | Lactobacillus crispatus | 3 | 92.8 | 78.5–100 | 12.4 |
| Undibacterium oligocarboniphilum A | 1 | 14.4 | n.a. | n.a. | |
| Pseudomonas saccharophila | 1 | 2.3 | n.a. | n.a. | |
| Undibacterium ligocarboniphilum A | 1 | 1.5 | n.a. | n.a. | |
| Unidentified species | 1 | 1.3 | n.a. | n.a. | |
| Ralstonia pickettii A | 1 | 1.0 | n.a. | n.a. | |
| Asinibacterium lactis | 1 | 0.4 | n.a. | n.a. | |
| Lactobacillus vaginalis | 1 | 0.3 | n.a. | n.a. | |
| Staphylococcus capitis | 1 | 0.2 | n.a. | n.a. | |
| Methylobacterium oryzae A | 1 | 0.1 | n.a. | n.a. | |
| UR67 (105) | Escherichia coli | 3 | 66.1 | 62.4–70.1 | 3.9 |
| Aerococcus urinae | 3 | 26.8 | 22.5–29.5 | 3.8 | |
| Enterococcus sp. | 3 | 8.5 | 7.5–9.2 | 0.9 | |
| UR68 (104) | Lactobacillus gasseri | 3 | 55.5 | 50.9–62.4 | 6.1 |
| Escherichia coli | 3 | 36.9 | 34.4–41.8 | 4.3 | |
| Streptococcus pasteurianus | 3 | 5.2 | 2.3–8.7 | 3.2 | |
| Enterococcus sp. | 3 | 1.0 | 0.3–2.0 | 0.9 | |
| Veillonella sp. | 2 | 0.2 | 0.2–0.2 | 0.0 | |
| Unidentified species | 1 | 3.6 | n.a. | n.a. | |
| Facklamia sp A | 1 | 0.2 | n.a. | n.a. | |
| UR69 (105) | Klebsiella pneumoniae | 3 | 77.5 | 73.1–85.5 | 6.9 |
| Aerococcus urinae | 3 | 12.8 | 1.8–25.1 | 11.7 | |
| Actinotignum sanguinis | 3 | 8.6 | 1.3–21.6 | 11.3 | |
| Lactobacillus crispatus | 3 | 1.0 | 0.1–2.6 | 1.4 |
ABacterial microorganism previously reported as contamination of DNA extraction kits, PCR and other laboratory reagents10. Bn.a., not assigned.