Table 2.
Sequence data and diversity indexes
|
Sample type |
Characteristics |
Sequence type |
|||
|---|---|---|---|---|---|
|
Bacterial (16S) |
Fungal (ITS1) |
||||
| TB | Controls | TB | Controls | ||
|
Nasal |
Total sequencesa |
124,977 |
106,729 |
76,480 |
73,858 (4) |
| Observed OTUs |
318 |
348 |
378 |
345 |
|
| Chao1 |
708 |
627 |
684 |
585 |
|
| Shannon (H') |
3.0* |
4.2* |
6.9 |
6.6 |
|
|
Oropharynx |
Total sequencesa |
140,987 |
95,693 |
29,759 |
22,376 (3) |
| Observed OTUs |
577 |
882 |
98 |
131 |
|
| Chao1 |
1262 |
1941 |
153 |
209 |
|
| Shannon (H') |
4.8 |
5.8 |
3.8 |
4.8 |
|
| Sputum | Total sequences |
120,681 |
ND |
66,278 |
ND |
| Observed OTUs |
827 |
ND |
102 |
ND |
|
| Chao1 |
1857 |
ND |
154 |
ND |
|
| Shannon (H') | 6.1 | ND | 3.4 | ND | |
ND not available. aNumber in parenthesis indicates samples for which sequences were obtained, if less than 6. *p < 0.05 (U Mann-Whitney) indicates significance between TB patients and healthy controls for 16S rRNA gene sequences.