Maukonen et al. Fecal microbiota and immunologicaldysregulation of pediatricpatients with inflammatoryboweldisease
Table S1. Primers used in the present study.
Target group
Short name
Probe / primer
Use
Sequence (5’ → 3’)
Reference
predominant bacteria a
Univ
U968-f +GC
PCR-DGGE
CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGC
[1]
ACGGGGGGAACGCGAAGAACCTTA
predominant bacteria a
U1401-r
PCR-DGGE
CGGTGTGTACAAGACCC
[1]
predominant bacteria b
534R
qPCR
ATTACCGCGGCTGCTGG
[2]
predominant bacteria b
358F
qPCR
CCT ACG GGA GGC AGC AG
[2]
Erec-group
Ccoc-f
PCR-DGGE
AAATGACGGTACCTGACTAA
[3]
Erec-group
Ccoc-r + GC
PCR-DGGE
CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGC
[4]
Eubacterium rectale – Blautia
Univ
coccoides group c
Eubacterium rectale – Blautia
ACGGGGGGCTTTGAGTTTCATTCTTGCGAA
coccoides group c
Erec-group
g-Ccoc-F
qPCR
AAATGACGGTACCTGACTAA
[5]
Erec-group
g-Ccoc-R
qPCR
CTTTGAGTTTCATTCTTGCGAA
[5]
Clostridium leptum group d
Clept-group
Clept-933 f
PCR-DGGE
GCACAAGCAGTGGAGT
[5]
Clostridium leptum group d
Clept-group
Clept-1240-r
GTT TTR TCA ACG GCA GTC
[6]
Clostridium leptum group d
Clept-group
Clept-1240-r+GC
CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGC
[7]
Eubacterium rectale – Blautia
coccoides group c
Eubacterium rectale – Blautia
coccoides group c
PCR-DGGE
ACGGGGGGGTTTTRTCAACGGCAGTC
Maukonen et al. Fecal microbiota and immunologicaldysregulation of pediatricpatients with inflammatoryboweldisease
Clostridium leptum group d
Clept-group
Clept-f
qPCR
GCACAAGCAGTCGAGT
[5]
Clostridium leptum group d
Clept-group
Clept-R3
qPCR
CTTCCTCCGTTTTGTCAA
[5]
genus Bacteroides
Bacteroides spp.
Bact596f
PCR-DGGE
TCA GTT GTG AAA GTT TGCG
[8]
GCA CTT AAG CCG ACA CCT
[9]
CGCCCGGGGCGCGCCCCGGGCGGGGCGGGGGC
[7]
Bacto1080r
genus Bacteroides
Bacteroides spp.
Bacto1080r + GC
PCR-DGGE
ACGGGGGGGCACTTAAGCCGACACCT
genus Bacteroides
Bacteroides spp
g-Bfra-F
qPCR
ATAGCCTTTCGAAAGRAAGAT
[5]
genus Bacteroides
Bacteroides spp
g-Bfra-R
qPCR
CCAGTATCAACTGCAATTTTA
[5]
Bifidobacteria
Bif
Bif164-f
PCR-DGGE
GGGTGGTAATGCCGGATG
[10]
Bifidobacteria
Bif
Bif662-GC-r
PCR-DGGE
CGCCCGCCGCGCGCGGCGGGCCGGGCGGGGGC
[10]
ACGGGGGGCCACCGTTAGACCGGGAA
Bifidobacteria
Bif
Bifid-f
qPCR
CTCCTGGAAACGGGTGG
[3]
Bifidobacteria
Bif
Bifid-r
qPCR
GGTGTTCTTCCCGATATCTACA
[3]
Maukonen et al. Fecal microbiota and immunologicaldysregulation of pediatricpatients with inflammatoryboweldisease
Lactobacillus-groupe
Lac
Lac1
PCR-DGGE
AGCAGTAGGGAATCTTCCA
[8]
Lactobacillus-groupe
Lac
Lac2GC
PCR-DGGE
CGCCCGCCGCGCCCCGCGCCCGGCCCGCCG
[8]
CCCCCGCCCCATTYCACCGCTACACATG
Atopobium-groupf
Ato
Atopo-f
qPCR
GGGTTGAGAGACCGACC
[5]
Atopobium-groupf
Ato
Atopo-r
qPCR
CGGRGCTTCTTCTGCAGG
[5]
sequencing
7F
seq.
AGAGTTTGATYMTGGCTCAG
[10]
sequencing
1510R
seq.
TACGGYTACCTTGTTACGACTT
[10]
a
Partial 16S rRNA gene (V6-V8 hypervariable region)
b
Partial 16S rRNA gene (V3-V5 hypervariable region)
c
Lachnospiraceae, Clostridial phylogenetic clusters XIVa [11]
d
Ruminococcaceae, Clostridial phylogenetic clusters IV [11]
e
Lactobacillus-group comprises of the genera Lactobacillus, Leuconostoc, Pediococcus, and Weissella
f
Atopobium-group comprises e.g. of genera Atopobium, Eggerthella, and Collinsella
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