01) (Table 2). As a negative control, we performed two independent PCR-LDR-UA experiments using double distilled water, instead of genomic DNA, as sample. As expected, no positive

signal was detected. The ratio between the signal intensities of the specific probes and the blank intensity (SNRs) averaged 206.9 ± 185.7, whereas the ratio between all the other probes and the blank intensity (SNRns) averaged 2.1 ± 1.4. Therefore, the ratio between specific and non-specific probes resulted more than 100 fold on average. Table 2 Specificity test. DNA Target R428 positive signal SNR other SNR spec p-valus spec B. fragilis ATCC25285 Adriamycin datasheet Bacterodes/Prevotella 0.85 30.81 9.35E-05     0.53 21.45 7.39E-04 B. thetaiotaomicrom ATCC29143 Bacterodes/Prevotella 0.45 61.44 2.56E-04     1.66 347.24 9.10E-06 L. gasseri DSM20243 Lactobacillaceae 0.30 5.58 4.98E-03     1.56 20.59 6.58E-03 P. melaninogenica ATCC25845 Bacterodes/Prevotella 1.54 480.24 6.02E-08     0.90 266.63 3.74E-09 B. subtilis DSM704 Bacillus subtilis 7.93 637.39 1.56E-09     5.62 350.10 1.47E-05 E. coli ATCC11105 Enterobacteriaceae 3.27 555.04 8.65E-08     2.59 222.39 4.50E-07 P. mirabilis DSM4479 Proteus, Enterobacteriaceae 2.42 703.22 7.74E-09     2.03 497.10 1.97E-09 B. bifidum DSM20456 Bifidobacteriaceae 2.67 289.39 4.78E-11     2.23 407.10 2.40E-08 L. casei DSM20011 Lactobacillaceae, L. casei 2.59 PI3K Inhibitor Library 125.13 1.01E-04     2.26 134.78

5.92E-04 Y. enterocolitica (faecal isolate) Yersinia enterocolitica, Enterobacteriaceae 1.53 231.33 1.01E-05     2.89 340.20 1.61E-06 B. cereus DSM31 Tolmetin Bacillus cereus 2.83 193.85 1.53E-06     2.49 196.82 4.16E-03 B. adolescentis ATCC15703 Bifidobacteriaceae 4.10 732.95 3.95E-10     2.90 338.59 5.59E-07 L. ramnosus DSM20021 Lactobacillaceae, L. casei 2.40 101.76 1.41E-03     4.23 177.70 4.62E-07 L. delbrueckii DSM20074 Lactobacillaceae 3.77 210.11 2.24E-08     3.10 121.93 6.27E-08 L. pentosus DSM20314 Lactobacillaceae 3.05 131.65 4.58E-09     1.63 58.30 5.32E-07 L. acidophilus DSM20079 Lactobacillaceae 2.39 68.49 8.70E-05     2.66 78.50 5.88E-06 L. reuteri DSM20016 Lactobacillaceae

3.17 150.57 4.66E-09     1.74 83.60 1.98E-07 L. plantarum DSM21074 Lactobacillaceae, L. plantarum 2.12 197.32 3.79E-09     2.09 148.35 2.77E-08 C. difficile ATCCBAA1382 Clostridium XI, Clostridium difficile 1.12 238.87 4.88E-04     0.80 126.38 1.96E-03 C. jejuni ATCC33292 Campylobacter jejuni 0.70 19.89 5.29E-03     0.91 28.44 5.69E-03 V. parvula ATCC10790 Veillonella, Clostridium IX 1.12 205.66 1.57E-04     0.99 140.95 1.39E-04 B. breve DSM20091 Bifidobacteriaceae 2.22 570.01 6.22E-05     1.69 289.07 2.72E-04 B. longum ATCC15707 Bifidobacteriaceae, B. longum 1.76 341.94 1.64E-03     0.66 134.86 4.26E-02 R.