TABLE 1.
Characterization of DNA sequences detected in this study after PCR or RT-PCR amplification from total nucleic acids extracted from feed (tobacco leaves), eggs, larval guts, or feces of Manduca sexta
| Band | Name of cloned sequence | Accession no. | Length of sequence (bp) | Closest relative(s) (% sequence identity) | Order (phylum or class) | Comment |
|---|---|---|---|---|---|---|
| D-SSCPa | ||||||
| 1 | Ms01aDNA | AM910351 | 369 | Burkholderia sp., Ralstonia sp., Cupriavidus sp. (all 99.7) | Burkholderiales (Betaproteobacteria) | Also in RNA profiles (band 5) |
| 2 | Ms08cDNA | AM910352 | 371 | Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus saccharolyticus (all 100) | Lactobacillales (Firmicutes) | Also in RNA profiles (band 6) |
| 3 | Ms09aDNA | AM910353 | 370 | Citrobacter sedlakii (99.7) | Enterobacteriales (Gammaproteobacteria) | Also in RNA profiles (band 9) |
| 4 | Ms10aDNA | AM910354 | 367 | Various uncultured clones (100) | Sphingobacteriales (Bacteroidetes) | Only in DNA profiles |
| R-SSCPb | ||||||
| 5 | Ms18cRNA | AM910355 | 369 | Burkholderia sp., Ralstonia sp., Cupriavidus sp. (all 98.6) | Burkholderiales (Betaproteobacteria) | 98.4% identical to band 1 |
| 6 | Ms21aRNA | AM910356 | 371 | E. gallinarum, E. casseliflavus, E. saccharolyticus (all 99.7) | Lactobacillales (Firmicutes) | 99.7% identical to band 2 |
| 7 | Ms22aRNA | AM910357 | 369 | Caulobacter sp. (100) | Caulobacterales (Alphaproteobacteria) | Weak band, only in RNA profiles |
| 8 | Ms01cRNA | AM910358 | 370 | Various Pseudomonas spp. (99.2) | Pseudomonadales (Gammaproteobacteria) | Weak band, only in RNA profiles |
| 9 | Ms28cRNA | AM910359 | 370 | C. sedlakii (100) | Enterobacteriales (Gammaproteobacteria) | 100% identical to band 3 |
| S-R-SSCPc | ||||||
| 10 | Ms10bSIP | AM910360 | 370 | Enterobacter cloacae, Enterobacter aphidicola, Enterobacter aerogenes (all 100) | Enterobacteriales (Gammaproteobacteria) | Only SIP-SSCP profiles (heavy fraction, indicating activity) |
| 11 | Ms16cSIP | AM910361 | 371 | E. gallinarum, E. casseliflavus, E. saccharolyticus (all 99.7) | Lactobacillales (Firmicutes) | 100% identical to band 2 |
| 12 | Ms15aSIP | AM910362 | 370 | Uncultured Sphingomonas sp. (98.9) | Sphingomonadales (Alphaproteobacteria) | Only in SIP-SSCP profiles; however, not in fractions, indicating activity |
| 13 | Ms17cSIP | AM910365 | 365 | Flavobacterium hydatis, other Flavobacterium spp. (100) | Flavobacteriales (Bacteroidetes) | |
| 14 | Ms03bSIP | AM910363 | 369 | Delftia acidovorans (100) | Burkholderiales (Betaproteobacteria) | |
| 15 | Ms11cSIP | AM910364 | 371 | Bacillus licheniformis (100) | Bacillales (Firmicutes) |
a
D-SSCP, isolated from DNA-based PCR SSCP profiles.
b
R-SSCP, isolated from RNA-based RT-PCR SSCP profiles.
c
S-R-SSCP, isolated from SIP RNA-based RT-PCR SSCP profiles.