TABLE 1.
Detection frequencies and species correlations of resolved T-RF bandsa
| T-RF band length (bases) | % of patients with band | Bacterial species assignation |
|---|---|---|
| 59 | 62 | Craurococcus roseus |
| 61 | 44 | Rhizobium loti, Ochrobactrum anthropi, Peptostreptococcus anaerobius |
| 68 | 21 | Ralstonia gilardii |
| 92 | 9 | Bilophila wadsworthia |
| 93 | 3 | Desulfovibrio desulfuricans, Tistrella mobilis |
| 96 | 3 | Wolinella succinogenes, Campylobacter rectus, Bacteroides forsythus |
| 98 | 6 | Bacteroides gracilis |
| 102 | 57 | Prevotella loescheii, P. salivae, P. buccae, P. oris, Porphyromonas gingivalis |
| 104 | 71 | Porphyromonas endodontalis, Prevotella denticola, P. melaninogenica, P. nigrescens, P. veroralis, P. intermedia |
| 155 | 88 | Pseudomonas aeruginosa |
| 197 | 3 | Acinetobacter junii |
| 201 | 9 | Mycobacterium tuberculosis |
| 207 | 15 | Acinetobacter johnsonii |
| 208 | 3 | Pandoraea pulmonicola |
| 209 | 15 | Burkholderia cepacia complexb |
| 210 | 9 | Burkholderia gladioli |
| 211 | 15 | Abiotrophia paraadiacens |
| 213 | 12 | Actinomyces viscosus, A. naeslundii, Xanthomonas campestris, Morganella morganii, Neisseria species (N. meningitidis, N. gonorrhoeae), Xanthomonas hyacinthi, Pseudomonas aureofaciens, Legionella pneumophila |
| 214 | 9 | Stenotrophomonas maltophilia, Fusobacterium gonidiaformans |
| 215 | 6 | Aeromonas caviae, Abiotrophia defectiva |
| 225 | 6 | Flavobacterium indologenes |
| 238 | 18 | Staphylococcus aureus, S. epidermidis, S. cohnii, S. hominis |
| 256 | 3 | Lactobacillus murinus |
| 266 | 6 | Staphylococcus sciuri |
| 279 | 3 | Rhizobium radiobacter |
| 339 | 3 | Methylobacterium radiotolerans |
| 363 | 6 | Mycobacterium chelonae |
| 364 | 9 | Haemophilus paraphrophilus, H. influenzae, Actinobacillus actinomycetemcomitans |
| 367 | 3 | Mycobacterium flavescens |
| 372 | 15 | Salmonella enterica serovar typhimurium, Bifidobacterium pseudocatenulatum, Proteus mirabilis |
| 445 | 3 | Bordetella hinzii |
| 562 | 6 | Eubacterium saburreum |
| 563 | 6 | Halomonas variabilis |
| 566 | 18 | Comamonas testosteroni |
| 569 | 26 | Paracoccus halodenitrificans |
| 571 | 3 | Pseudomonas huttiensis |
| 574 | 35 | Ralstonia pickettii, Oligella urethralis |
| 576 | 6 | Streptococcus pneumoniae, S. salivarius, S. pyogenes, S. macedonicus, S. sanguinis |
| 585 | 32 | Selenomonas sputigena, Streptococcus intermedius |
| 587 | 6 | Peptococcus-like species oral clone JM048 |
| 588 | 9 | Veillonella parvula |
| 589 | 3 | Capnocytophaga sputigena |
| 590 | 3 | Streptococcus anginosus, Veillonella atypica, V. ratti |
| 843 | 3 | Alcaligenes xylosoxidans |
| 846 | 9 | Treponema pallidum |
a
T-RF bands were detected in the sample set, and corresponding species band sizes were predicted (as determined by software-driven analysis of published sequence data). The percentages of patients in the sample set in which each band was detected and the names of the species with which they are consistent are listed.
b
Sequences from genomovars B. cepacia, B. multivorans, B. stabilis, B. vietnamensis, B. ambifaria, and B. anthina of the B. cepacia complex were all subjected to in silico analysis. However, there was insufficient sequence data to derive in silico T-RFLP band size lengths for genomovars B. dolosa, B. pyrrocinia, B. ubonensisa, or B. cenocepacia.