Table 1 Target for probes and sequences of rRNA-targeting oligonucleotide probes and 16S rRNA gene targeting primers used in this study

Bacteria

S-D-bact-0338-a-A-18

5' GCT GCC TCC CGT AGG AGT 3'

Fluorescein

[37]

Enterobateria

GAM42a

5' GCC TTC CCA C(AT)TCGT TT 3'

Fluorescein

[38]

S-S-C.perfring-185-a-A-18

5'TGG TTG AAT GAT GAT GCC 3'

Cy3

[21]

Clostridium spp. ¹

S-S-C.paraputri-181

5' CAT GCG AAC GTA CAA TCT 3'

Cy3

This study

S-S-C. butyricum-663

5'AGG AAT TCT CCT TTC CTC 3'

Cy3

This study

S-S-C.diff-193-a-A-18

5'TGT ACT GGC TCA CCT TTG 3'

Cy3

[21]

Actinobacteria

pB-00182

5'TA TAG TTA CCA CCG CCG T 3'

Cy3

[39]

Lactobacillus & Enterococcus

Lab158

5'GGTAT TAJ CAY CTG TTTCCA3'

Cy3

[40]

Bifidobateria

pB-00037

5'CC AGT GGC TAT CCC TGT GTG AAG G3'

Cy3

[41]

PCR Primers

Bacteria

Bact64f

5'-CY TAA YRC ATG CAA GTC G-3'

[42]

Bacteria

Bact109r1

5'-YY CAC GYG TTA CKC ACC CGT-3'

[42]

Bacteria

PyroBact64f

5'-CAT GCA AGT CG-3'

Biotin C-6

This study