Table 1. Results of the high-throughput sequencing (reads and assignment) of bacterial (V1-V2 and V3-V4 16S targets) and fungal (ITS1 and ITS2) targets of 2 sputa from 2 patients (P1, P2) extracted using 2 protocolsa (Automated QIAsymphony Extraction [AQE] with DSP DNA midi kit and Manual PowerSoil® Extraction [MPE]).
| Overall | P1 Reads (%) | P2 Reads (%) | ||||
|---|---|---|---|---|---|---|
| Reads (%) | MPE | AQE | MPE | AQE | ||
| Reads assigned as bacteria | 93,451 | 20,908 | 10,366 | 35,055 | 27,122 | |
| 16S, | – At species level | 44,032 (47.1) | 20,379 (97.5) | 10,021 (96.7) | 7,852 (22.4) | 5,780 (21.3) |
| V1-V2 | – At genus level only | 48,521 (51.9) | 301 (1.4) | 212 (2.0) | 26,797 (76.4) | 21,211 (78.2) |
| – Unidentified bacteria | 898 (1) | 228 (1.1) | 133 (1.3) | 406 (1.2) | 131 (0.5) | |
| Nb of taxab | 25 | 18 | 17 | 12 | 12 | |
| Reads assigned as bacteria | 276,475 | 61,552 | 32,669 | 113,963 | 68,291 | |
| 16S, | – At species level | 220,980 (79.9) | 60,339 (98.0) | 31,697 (97.0) | 78,942 (69.3) | 50,002 (73.2) |
| V3-V4 | – At genus level only | 49,011 (17.7) | 908 (1.5) | 713 (2.2) | 31,164 (27.3) | 16,226 (23.8) |
| – Unidentified bacteria | 6484 (2.3) | 305 (0.5) | 259 (0.8) | 3857 (3.4) | 2063 (3.0) | |
| Nb of taxab | 41 | 32 | 29 | 20 | 15 | |
| Reads assigned as fungi | 65,112 | 20,926 | 22,832 | 6,940 | 14,414 | |
| – At species level | 63,477 (97.5) | 20,203 (96.5) | 22,667 (99.3) | 6,294 (90.7) | 14,313 (99.3) | |
| ITS1 | – At genus level only | 1,616 (2.5) | 711 (3.4) | 160 (0.7) | 646 (9.3) | 99 (0.7) |
| – Unidentified fungi | 19 (0.0) | 12 (0.1) | 5 (0.0) | 0 (0.0) | 2 (0.0) | |
| Nb of taxab | 5 | 5 | 5 | 4 | 3 | |
| Reads assigned as fungi | 191,349 | 34,033 | 56,206 | 23,279 | 77,831 | |
| – At species level | 154,347 (80.7) | 419 (1.2) | 55,566 (98.9) | 21,535 (92.5) | 76,827 (98.7) | |
| ITS2 | – At genus level only | 36,982 (19.3) | 33,609 (98.8) | 635 (1.1) | 1,738 (7.5) | 1,000 (1.3) |
| – Unidentified fungi | 20 (0.0) | 5 (0.0) | 5 (0.0) | 6 (0.0) | 4 (0.0) | |
| Nb of taxab | 10 | 8 | 7 | 7 | 7 | |
a- Methods used the same starting quantities of sample and final volumes were equal.
b- At genus level.