Table 1 Oligonucleotides and optimized PCR conditions of the pathogen panel applied in this study

Bacteroides-Prevotella-Porphyromonas (140 bp, 3 mM,55 °C, SYBR)

F:5′-GGTGTCGGCTTAAGTGCCAT-3′

R:5′-CGGA(C/T)GTAAGGGCCGTGC-3′

[15]

Bifidobacterium spp. (243 bp, 3 mM, 55 °C, SYBR)

F:5′-TCGCGTC(C/T)GGTGTGAAAG-3′

R:5′-CCACATCCAGC(A/G)TCCAC-3′

[15]

Campylobacter spp. (246 bp, 3 mM, 55 °C, SYBR)

F:5′-GGATGACACTTTTCGGAG-3′

R:5′-AATTCCATCTGCCTCTCC-3′

[15]

C. difficile (157 bp, 3 mM, 55 °C, SYBR)

F:5′-TTGAGCGATTTACTTCGGTAAAGA-3′

R:5′CCATCCTGTACTGGCTCACCT-3′

[15]

C. perfringens group (120 bp, 3 mM, 55 °C, SYBR)

F:5′-ATGCAAGTCGAGCGA(G/T)G-3′

R:5′-TATGCGGTATTAATCT(C/T)CCTTT-3′

[15]

Enterococcus spp. (144 bp, 3 mM, 55 °C, SYBR)

F:5′-CCCTTATTGTTAGTTGCCATCATT-3′

R:5′-ACTCGTTGTACTTCCCATTGT-3′

[15]

Veillonella spp. (343 bp, 3 mM, 55 °C, SYBR)

F:5′-A(C/T)CAACCTGCCCTTCAGA-3′

R:5′-CGTCCCGATTAACAGAGCTT-3′

[15]

B. fragilis (176 bp, 3 mM, 55 °C, SYBR)

F:5′-GAAAGCATTAAGTATTCCACCTG-3′

R:5′-CGGTGATTGCTCACTGACA-3′

[16]

E. coli subgroup (340 bp, 3 mM, 61 °C, SYBR)

F:5′-GTTAATACCTTTGCTCATTGA-3′

R:5′-ACCAGGGTATCTAATCCTGTT-3′

[16]

Lactobacillus spp. (341 bp, 2 mM, 55 °C, SYBR)

F:5′-AGCAGTAGGGAATCTTCCA-3′

R:5′-CACCGCTACACATGGAG-3′

[17]

B. bifidum (278 bp, 2 mM, 55 °C, SYBR)

F:5′-CCACATGATCGCATGTGATTG-3′

R:5′-CCGAAGGCTTGCTCCCAAA-3′

[18]

B. longum group (106 bp, 4 mM, 55 °C, SYBR)

F:5′-CAGTTGATCGCATGGTCTT-3′

R:5′-TACCCGTCGAAGCCAC-3′

[18]

L. acidophillus (575 bp, 55 °C, SYBR)

F:5′-CACTTCGGTGATGACGTTGG-3′

R: 5′-CGATGCAGTTCCTCGGTTAAGC-3′

[19]