. 2016 Feb 21;22(7):2219–2241. doi: 10.3748/wjg.v22.i7.2219

Table 1.

Perturbations in the intestinal microbiotain irritable bowel syndrome patients

Ref.	Methods	N° of Pts.	Diagnostic criteria	Results in IBS in comparison with healthy subjects
Dlugosz et al[38]	qPCR (small bowel)	35	Rome II	No differences
Balsari et al[39]				↓Coliforms
				↓Lactobacilli
				↓ Bifidobacteria
Si et al[40]	Culture	25	Rome II	↓Bifidobacteria
Si et al[40]	Culture	25	Rome II	↑Enterobacteriaceae
Malinen et al[41]	qPCR	27	Rome II	↑ Veillonellain C-IBS
Malinen et al[41]	qPCR	27	Rome II	↓Lactobacillus in D-IBS
Mättö et al[42]	Culture/DGGE	26	Rome II	↑ Aerobes
Mättö et al[42]	Culture/DGGE	26	Rome II	Temporal instability
Swidsinski et al[43]	FISH	20	A-IBS	↑ Mucosal bacteria
			C-IBS	↑Eubacteriumrectale
			D-IBS	↑Clostridium coccoides
Maukonen et al[44]	PCR-DGGE	16	A-IBS	Higher instability of the bacterial population
			C-IBS	↑Clostridial groups
			D-IBS
Kassinen et al[45]	16S ribosomal RNA gene cloning	24	Rome II	Significant differences in several bacterial genera belonging to the genera Coprococcus, Collinsella and Coprobacillus
Lyra et al[46]	16S ribosomal RNA gene cloning	20	A-IBS C-IBS D-IBS	↑Clostridium thermosuccinogenes in D-IBS ↑Ruminococcus torques in D-IBS ↑Ruminococcus bromii-like in C-IBS
Krogius-Kurikka et al[47]	16S ribosomal RNA gene cloning	10	Rome II	↑Proteobacteria and Firmicutes in D-IBS
Krogius-Kurikka et al[47]	16S ribosomal RNA gene cloning	10	Rome II	↓Actinobacteria and Bacteroidetes in D-IBS
Kerckhoffs et al[48]	FISH, PCR	41	A-IBS	↓Bifidobacteria
			C-IBS
			D-IBS
Carroll et al[49]	16S ribosomal RNA gene cloning	2	Rome III	↑Bacteroidetes ↑Proteobacteria
Salonen et al[50] Review
Tana et al[51]	Culture	26	Rome II	↑Lactobacillus
Tana et al[51]	qPCR	26	Rome II	↑ Veillonella
Carroll et al[52]	qPCR	10	Rome III	↓Aerobicbacteria
Carroll et al[52]	qPCR	10	D-IBS	↑Lactobacillus
Codling et al[53]	16S rRNA-DGGE	47	Rome II	↓Bacterial richness
Ponnusamy et al[54]	rRNA-specific 16S rRNA-DGGE	54	Rome II	Same total bacterial quantity Higher diversity of Bacteroidetes and Lactobacilli
Ponnusamy et al[54]	PCR			Lower diversity of Bifidobacter and Clostridium coccoides
Kerckhoffs et al[55]	16S rRNA-DGGE	37	Rome II	↑Pseudomonas aeruginosa
Kerckhoffs et al[55]	qPCR	37	Rome II	↑Pseudomonas aeruginosa
Rajilić-Stojanović et al[56]	16S rRNA	62	Rome II	↑Ratio of the Firmicutes to Bacteroidetes
	qPCR			↑Dorea, Ruminococcus, Clostridium spp
				↓Bacteroidetes, Bifidobacterium, Faecalibacterium spp
Carroll et al[57]	16S rRNA	16	Rome III D-IBS	Lower biodiversity of microbes
Carroll et al[58]	16S rRNA	23	D-IBS	↓Bacterial richness
				↑Enterobacteriaceae
				↑Proteobacteria
				↓Faecalibacterium
Parkes et al[59]	FISH	47	Rome III	More total bacteria numbers
Parkes et al[59]	FISH	47	Rome III	↑Bacteroides, Clostridia coccoides-Eubacteriumrectale
Jeffery et al[60]	16S rRNA	37	Rome II	A sub-group of IBS showed normal-like microbiota
Jeffery et al[60]	16S rRNA	37	Rome II	A sub-group of IBS showed large microbiota-wide changes with ↑Firmicutes and ↓Bacteroidetes
Chassard et al[61]	FISH/16S rDNA	14	Rome II	↑Enterobacteriaceae
	Functional approaches		Rome III	↑Suphate-reducing bacteria
			C-IBS	↓Lactic acid bacteria population (bifidobacteria and to a lesser extent, lactobacilli)
König et al[62] Review
Sundin et al[63]	16s rRNA	19	Rome III	↑Bacteroidetes in the PI-IBS group (13 patients) ↑Firmicutes (more specifically Clostridium in IBS)

IBS: Irritable bowel syndrome; IBS-D: Diarrhea predominant IBS; IBS-C: Constipation predominant IBS; A-IBS: Alternate IBS; PI-IBS: Post-infectious-IBS; DGGE: Denaturing gradient gel electrophoresis; PCR: Polymerase chain reaction; FISH: Fluorescence in situ hybridization.