TABLE 1.
Identities of strains isolated during curing, as determined by three independent methods
| Strain typea | Biolog identification (similarityb) | DGGE identificationc | Closest cultured relative,d GenBank accession no. (% similarity) | Curing stage(s)e at:
|
|
|---|---|---|---|---|---|
| Tulungagung | Payung | ||||
| 1 | B. licheniformis (0.33–0.49) | B. licheniformis (upper bandf) | B. licheniformis, AF276309 (99.0) | A, Sw, R, C | C |
| B. licheniformis, AF276309 (98.1) | |||||
| 2 | B. subtilis (0.29–0.72) | B. subtilis | B. subtilis, Z99104 (97.0) | G, A, Sw, R, C | A, Sw, R, C |
| 3 | B. cereus (0.03–0.16) | NDh | B. firmus, D16268 (96.8) | A, Sw, R | |
| 4 | B. pumilis (0.61) | ND | B. pumilis, AF260751 (98.0) | A, Sw, R | |
| 5 | ND | ND | B. firmus, AJ229200 (97.2) | A, Sw, R | |
| 6 | B. smithii (0.92–0.99g) | B. smithii | ND | A, Sw, R | |
The Type numbers refer to the numbered bands in Fig. 5.
Significant similarities (>0.5) are shown in boldface.
DGGE was performed by using two primer sets: one amplifying the V3 region, the second amplifying the V6-V8 region. Results were compared to DSM type strains.
Determined based on 16S rDNA sequence homology. GenBank accession numbers for 16S rDNA sequences of the isolated strains are mentioned in Materials and Methods.
Abbreviations are as defined in Fig. 2.
B. licheniformis type strain (DSM13) and isolate both showed two bands in DGGE after amplification of the V3 region; only the upper band matched. Clones corresponding to both bands were sequenced.
B. smithii is not in the Biolog database; profiles were compared to that of the type strain DSM4216, incubated at 55°C.
ND, not determined.