Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients

Table 1 Genus-specific probes used for FISH analysis

Probe	Target group	Ref.
EUB 338	Total bacteria	[44]
Bac 303	Bacteroides-Prevotella group	[4546]
Bif 164	Bifidobacterium	[12]
Erec 482	Clostridium coccoides-Eubacterium rectale group	[47]
Chis 150	Clostridium histolyticum group	[47]
Clit 135	Clostridium lituseburense group	[47]
Cld 73	Clostridium difficile	This study: CGCCGCTCTTTACCGAAGT
Fprau 645	Faecalibacterium prausnitzii	[4648]
Lab 158	Lactobacillus-Enterococcus group	[49]

Table 2 FISH analysis of the composition of the fecal microbiota of HS, IBS patients and IBS subgroups

Probe	HS	IBS	IBS-A	IBS-D	IBS-C
Fprau 645	12.0 ± 2.1	9.2 ± 0.80	10.6 ± 1.6	8.2 ± 1.4	8.6 ± 1.2
Erec 482	16.6 ± 5.4	11.7 ± 2.5	6.4 ± 1.3	7.1 ± 1.2	20.5 ± 5.8
Bif 164	8.3 ± 1.9	4.2 ± 1.3a	1.7 ± 0.63	7.9 ± 5.2	4.5 ± 0.94
Lab 158	4.7 ± 0.88	4.0 ± 0.78	2.0 ± 0.38	4.0 ± 1.7	6.0 ± 1.5
Chis 150	2.4 ± 0.43	2.1 ± 0.57	2.0 ± 0.61	1.6 ± 0.37	2.4 ± 1.4
Bac 303	1.5 ± 0.89	3.6 ± 1.5	0.41 ± 0.21	4.4 ± 3.3	5.7 ± 2.8
Cld73	0.88 ± 0.28	0.43 ± 0.09	0.61 ± 0.16	0.32 ± 0.15	0.21 ± 0.08
Clit 135	0.39 ± 0.10	0.09 ± 0.03a	0.06 ± 0.03	0.09 ± 0.04	0.11 ± 0.06
Sum	44.4 ± 6.85	32.1 ± 3.27	22.7 ± 2.30	28.3 ± 5.90	43.5 ± 5.89

^aP < 0.05 vs HS. Data are expressed as percentage, mean ± SE.

Table 3 Real time PCR analysis of fecal bifidobacteria in HS, IBS patients and IBS subgroups

	HS	IBS	IBS-A	IBS-D	IBS-C
B. catenulatum	19.31 ± 2.5	6.24 ± 0.6b	6.57 ± 1.1b	5.67 ± 0.8b	6.49 ± 1.2b
B. adolescentis	17.05 ± 2.5	15.96 ± 1.6	16.86 ± 3.4	16.73 ± 1.8	14.06 ± 3.05
B. bifidum	2.1 × 10-4± 1.4 × 10-4	9.1 × 10-4± 6.3 × 10-4	3.3 × 10-4± 2.2 × 10-4	1.9 × 10-3± 1.8 × 10-3	4.5 × 10-4± 3.1 × 10-4
B. longum	7.11 ± 1.4	7.30 ± 0.8	6.68 ± 1.4	8.71 ± 1.7	6.45 ± 1.33

^bP < 0.001 vs HS. Data are expressed as percentage, mean ± SE.

Table 4 Duodenal mucosa-associated bifidobacteria in HS, IBS patients and IBS subgroups

	HS	IBS	IBS-A	IBS-D	IBS-C
B. catenulatum	17.04 ± 2.3	4.85 ± 0.5b	5.26 ± 0.9b	4.26 ± 0.7b	5.04 ± 1.0b
B. adolescentis	15.68 ± 2.3	13.90 ± 1.4	14.66 ± 2.7	14.58 ± 1.7	12.21 ± 3.0
B. bifidum	6.09 ± 0.9	5.13 ± 0.8	5.36 ± 1.7	4.43 ± 1.1	5.68 ± 1.3
B. longum	6.88 ± 1.3	7.27 ± 0.8	5.84 ± 1.3	9.01 ± 1.6	6.88 ± 1.40

^bP < 0.001 vs HS. Data are expressed as percentage, mean ± SE.