Table 2.
Bacterial species identified by NGS of 16S–23S rRNA encoding region using three different data analysis approaches and 16S rRNA gene Sanger sequencing and culturing.
| NGS of 16S–23S rRNA encoding region | Conventional methods | |||||
|---|---|---|---|---|---|---|
| De novo assembly+BLAST (cut-off: 0.3%) | OTU clustering (cut-off: 0.2%) | Mapping (cut-off: 0.4%) | 16S rRNA gene Sanger sequencing | Culturing | ||
| Sample number | Bacteria (relative abundance, %) | Bacteria (relative abundance, %) | Bacteria (relative abundance, %) | Bacteria | Bacteria | |
| 1# | Cutibacterium acnes (0.5%) | Negative | Negative | Streptococcus sp. | Cutibacterium acnes + <1 saccharolyticus¥ | |
| 3# | Negative | Negative | Gemella sp. (0.5%) | Negative | Negative | |
| 6## | Negative | Variovorax paradoxus (0.3%) | Negative | Negative | Negative | |
| 10# | Enterococcus faecium (0.7%) | Enterococcus faecium (1.9%) | Negative | Tropheryma whipplei | Negative | |
| Cutibacterium acnes (0.4%) | ||||||
| 11# | Cutibacterium acnes (0.4%) | Negative | Negative | Negative | Negative | |
| 15## | Cutibacterium sp. (0.4%) | Negative | Negative | Negative | Negative | |
| 17# | Cutibacterium acnes (0.7%) | Negative | Negative | Tropheryma whipplei | Negative | |
| 18# | Streptococcus sp. (95.8%) | Streptococcus sp. (52.4%) | Streptococcus sp. (48.1%) | Streptococcus sp. | Negative | |
| Bordetella sp. (0.32%) | Streptococcus pneumoni ae (9.2%) | Streptococcus australis (15.1%) | ||||
| Streptococcus australis (8.4%) | ||||||
| Streptococcus mitis (7.7%) | ||||||
| Streptococcus suis (6.1%) | ||||||
| Streptococcus parasanguinis (5.4%) | ||||||
| Streptococcus agalactiae (3.0%) | ||||||
| Streptococcus anginosus (2.5%) | ||||||
| Streptococcus ictaluri (2.1%) | ||||||
| Streptococcus cristatus (1.6%) | ||||||
| Streptococcus intermedius (1.2%) | ||||||
| 20## | Ureaplasma parvum (74.3%) | Ureaplasma parvum (79.8%) | Ureaplasma parvum (69.1%) | Ureaplasma parvum | Negative | |
| Ureaplasma urealyticum (16.6%) | Ureaplasma urealyticum (8.5%) | |||||
| 21## | Ureaplasma parvum (61.1%) | Ureaplasma parvum (78.9%) | Ureaplasma parvum (60.6%) | Ureaplasma parvum | Negative | |
| Ureaplasma urealyticum (15.9%) | Ureaplasma urealyticum (8.0%) | |||||
| 23# | Negative | Negative | Negative | Negative | Cutibacterium acnes<< 1 | |
| 24# | Negative | Negative | Negative | Cutibacterium acnes | Negative | |
| 25# | Streptococcus dysgalactiae (88.9%) | Streptococcus dysgalactiae (85.3%) | Streptococcus | Streptococcus | Negative | |
| dysgalactiae (81.4%) | dysgalactiae | |||||
| Streptococcus pyogenes (7.7%) | Streptococcus pyogenes (6.6%) | |||||
| Streptococcus agalactiae (6.5%) | Streptococcus canis (1.5%) | |||||
| Streptococcus suis (0.8%) | ||||||
| Streptococcus ictaluri (0.5%) | ||||||
| 26# | Streptococcus sanguinis (80.2%) | Streptococcus sanguinis (75.9%) | Streptococcus sanguinis (65.8%) | Streptococcus mitis | Negative | |
| Streptococcus anginosus (8.6%) | Streptococcus gordonii (1.9%) | |||||
| Streptococcus cristatus (3.8%) | Streptococcus parasanguinis (1.1%) | |||||
| Streptococcus parasanguinis (3.6%) | Streptococcus sp. (1.0%) | |||||
| Streptococcus agalactiae (2.6%) | Streptococcus anginosus (0.9%) | |||||
| Streptococcus pneumoniae (1.6%) | Streptococcus constellatus (0.9%) | |||||
| Streptococcus constellatus (0.8%) | Streptococcus cristatus (0.9%) | |||||
| Streptococcus gordonii (0.4%) | Streptococcus infantis (0.5%) | |||||
| 27## | Actinotignum schaalii (1.4%) | Actinotignum schaalii (17.5%) | Actinotignum schaalii (14.2%) | Actinotignum schaalii | Negative | |
| Actinotignum sp. (10.0%) | Aerococcus urinae (13.9%) | Aerococcus urinae (7.4%) | ||||
| Aerococcus urinae (6.2%) | ||||||
| Cutibacterium acnes (1.0%) | ||||||
| Time∗ | CLC analysis | ∼1 h 20 min | ∼3 h | ∼2 h 30 min | ||
| Hands on | ∼45 min | ∼1 h | ∼4 h | |||
| Total | ∼2 h 5 min | ∼4 h | ∼6 h 30 min | |||
∗Analysis time is for all 30 samples (including positive and negative control) using a i7-6700 CPU @ 3.40 GHz, 32 GB RAM, 64-bit operating system computer. ¥In later analysis, Cutibacterium acnes was identified. #Tissue sample (heart valve); ##Fluid sample; Cutibacterium acnes had been formerly referred to as Propionibacterium acnes.