Bacterial concentrations, amenability to fluorescence in situ hybridisation (FISH), biofilm structure, and composition
| Pancreatic duct (n = 9) | Narrowed stent ends (n = 44) | Partially occluded stent ends (n = 33) | Occluded stent ends (n = 19) | Brown/mixed gall stones (n = 27) | |
|---|---|---|---|---|---|
| A = number (%) of patients colonised with a specific group. | |||||
| B = mean per cent of all bacteria amenable to FISH positively hybridised with a group specific probe. | |||||
| C = maximal per cent of all bacteria amenable to FISH (Eub 338 + 4,6-diamidino-2-phenylindole (DAPI) stain) positively hybridised with a group specific probe. | |||||
| *Numbers are given after lysozyme treatment. | |||||
| Amenability to FISH | |||||
| % of bacteria amenable to FISH | 95 | 60–90 | 10–30 | <1 | <0.1 |
| Time necessary for FISH (h) | 1–2 | 3–5 | >12 | >12 | >12 |
| Time until exhaustion of Cy3 fluorescence (s) | 60 | 10–20 | <10 | <10 | <3 |
| Time necessary for DAPI stain (min) | 1 | 10–60 | 3–6 h | >12 h | >12 h |
| Biofilm structure | |||||
| Mean/max concentrations of all bacteria (/ml) | 2×108/1×1010 | 7×107/2×108 | 9×105/4×107 | 2×105/8×107 | |
| % of bacteria within a mixed multispecies biofilm | 30–40 | >90 | >90 | <30 | <10 |
| % of bacteria organised in islands of the same group | 30–70 | 5 | <1 | <1 | <1 |
| % singular bacteria scattered over microscopic field | <5 | <1 | <1 | 70–90 | >90 |
| Group specific probes | |||||
| Alf1b | |||||
| A | 4 (44%) | 7 (16%) | 2 (6%) | ||
| B | 5% | 0.01% | <0.01% | 0 | 0 |
| C | 40% | 1% | 0.1% | ||
| Beta42a | |||||
| A | 0 | 2 (5%) | 0 | 0 | 0 |
| B | <0.01% | ||||
| C | 0.1% | ||||
| Gam42a | |||||
| A | 1 (11%) | 26 (59%) | 17 (51%) | 10 (52%) | 9 (33%) |
| B | <0.1% | 19% | 11% | 14% | 4% |
| C | 5% | 80% | 80% | 80% | 30% |
| Ec1531 | |||||
| A | 0 | 19 (44%) | 15 (45%) | 9 (47%) | 9 (33%) |
| B | 10% | 6% | 8% | 3% | |
| C | 60% | 60% | 80% | 20% | |
| Srb385 | |||||
| A | 2 (22%) | 19 (44%) | 10 (30%) | 4 (21%) | 0 |
| B | 0.5% | 0.1% | <0.01% | <0.01% | |
| C | 5% | 3% | 0.1% | 0.1% | |
| HGC | |||||
| A | 13 (30%) | 10 (30%) | 7 (36%) | 8 (29%) | |
| B | 0 | 1.3% | 2.4% | 2.0% | 1% |
| C | 30% | 40% | 20% | 10% | |
| LGC* | |||||
| A | 6 (66%) | 24 (54%) | 21 (63%) | 12 (63%) | 22 (81%) |
| B | 8% | 6.8% | 15% | 22% | 30% |
| C | 30% | 80% | 60% | 60% | 80% |
| Lab158 | |||||
| A | 4 (44%) | 20 (45%) | 21 (63%) | 9 (47%) | 10 (37%) |
| B | 1% | 2.5% | 2% | 10% | 5% |
| C | 10% | 20% | 40% | 25% | 40% |
| Strc493* | |||||
| A | 6 (66%) | 30 (68%) | 20 (60%) | 14 (73%) | 20 (74%) |
| B | 3% | 1% | 6% | 24% | 30% |
| C | 20% | 10% | 50% | 50% | 60% |
| Bif164 | |||||
| A | 2 (22%) | 9 (20%) | 12 (36%) | 5 (18%) | 0 |
| B | <0.01% | 1% | <0.1% | <0.01% | |
| C | 0.01% | 5% | 3% | 1% | |
| Erec482 | |||||
| A | 0 | 3 (7%) | 2 (6%) | 0 | 0 |
| B | 0.3% | 0.4% | |||
| C | 10% | 10% | |||
| Chis150 | |||||
| A | 1 (11%) | 12 (27%) | 10 (30%) | 11 (58%) | 0 |
| B | <0.1%/ | 0.2% | 0.1% | 0.03 | |
| C | 0.1% | 5% | 3% | 0.5% | |
| Clit135 | |||||
| A | 0 | 22 (50%) | 10 (30%) | 11 (58%) | 0 |
| B | 0.2% | 0.1% | 1% | ||
| C | 3% | 5% | 8% | ||
| CF319a | |||||
| A | 4 (44%) | 24 (55%) | 20(60%) | 5 (26%) | 0 |
| B | 8% | 1.5% | 1% | 0.3% | |
| C | 40% | 20 | 10% | 1% | |
| Bac303 | |||||
| A | 3 (33%) | 34 (77%) | 25 (76%) | 11 (58%) | 22 (81%) |
| B | 5% | 25% | 12% | 12% | 8% |
| C | 15% | 80% | 50% | 30 | 80 |