Table 3

Summary of culture and molecular studies of colonic microbiome

Study	Subject	Sample	Method	Patient group	Main finding	Country of study
Balsari et al 96	IBS (n=20) Ctrls (n=20)	Faeces	Culture	IBS	↓ Coliform bacteria ↓ Lactobacillus spp. ↓ Bifidobacterium spp.	Italy
Si et al 98	IBS (n=25) Ctrls (n=25)	Faeces	Culture	IBS	↓ Bifidobacterium ↑ Enterobacteriaceae ↓ C perfringens	China
Malinen et al 99	IBS (n=27) Ctrls (n=22)	Faeces	qPCR	IBS	↓ B catenulatum ↓ Cl coccoides group	Finland
				IBS-D	↓ Lactobacillus spp.
				IBS-C	↑ Veillonella spp. ↑ Lactobacillus spp.
Mättö et al 100	IBS (n=26) Ctrls (n=25)	Faeces	CulturePCR-DGGE	IBS	↑ Coliform bacteria ↑ Aerob to anaerob ratio ↓ Temporal stability	Finland
Maukonen et al 101	IBS (n=24) Ctrls (n=16)	Faeces	PCR-DGGE Affinity capture	IBS	↓ Temporal stability	Finland
Maukonen et al 101	IBS (n=24) Ctrls (n=16)	Faeces	PCR-DGGE Affinity capture	IBS-C	↓ Cl coccoides group	Finland
Kassinen et al 102	IBS (n=24) Ctrls (n=23)	Faeces	GC-profiling + sequencing of 16S rRNA genes qPCR	IBS	↓ Collinsella aerofaciens ↓ Cl cocleatum ↓ Coprococcus eutactus Subgroup-diff (D, C, M)	Finland
Rajilić-Stojanović103	IBS (n=20) Ctrls (n=20)	Faeces	Microarray	IBS	Proteobacteria and specific Firmicutes↑ Other Firmicutes, Bacteroidetes and bifidobacteria ↓	Finland
Kerckhoffs et al 104	IBS (n=41) Ctrls (n=26)	Faeces Duodenal mucosa	FISH qPCR	IBS	↓ Bifidobacterium spp. ↓ B catenulatum	The Netherlands
Krogius-Kurikka et al 105	IBS-D (n=10) Ctrls (n=23)	Faeces	GC-profiling + sequencing of 16S rRNA genes	IBS-D	↑ Proteobacteria ↑ Firmicutes ↓ Actinobacteria ↓ Bacteroidetes	Finland
Lyra et al 106	IBS (n=20) Ctrls (n=15)	Faeces	qPCR	IBS-D	↑ R torques 94% ↓ Cl thermosuccinogenes 85%	Finland
				IBS-C	↑ R bromii-like
				IBS-A	↓ R torques 93% ↑ Cl thermosuccinogenes 85%
Tana et al 107	IBS (n=26) Ctrls (n=26)	Faeces	Culture qPCR	IBS	↑ Veillonella spp. ↑ Lactobacillus spp.	Japan
Codling et al 108	IBS (n=41) Ctrls (n=33)	Faeces Colonic mucosa	PCR-DGGE	IBS	↑ Temporal stability No significant difference Faecal/mucosal	Ireland
Carroll et al 28	IBS-D (n=10) Ctrls (n=10)	Faeces Colonic biopsies	Culture qPCR	IBS-D	↓ Aerobic bacteria Lactobacillus spp.	USA
Noor et al 109	IBS (n=11) Ctrls (n=22) UC (n=13)	Faeces	PCR-DGGE + sequencing of 16S rRNA genes	IBS	↓ Bacterial species ↓ Biodiversity ↑ Biological variability of predominant bacteria	UK
Malinen et al 110	IBS (n=44)	Faeces	qPCR		R torques 94% symptom severity Other phylotypes neg assoc.	Finland
Ponnusamy et al 111	IBS (n=11) Ctrls (n=8)	Faeces	DGGE + qPCR of 16sRNA genes		↑ Diversity in Bacteroidetes & Lactobacilli ↑ Alanine & pyroglutamic acid & phenolic compounds	Korea
Rinttila et al 112	IBS (n=96) Ctrls (n=23)	Faeces	qPCR	IBS	S aureus (17%)	Finland
Saulnier et al 113	IBS (n=22) Ctrls (n=22) (Children)	Faeces	16s Metagenomic sequencing and DNA microarray	IBS	↑ γ Proteobacteria Classified IBS subtypes using sets of discriminant bacterial species	USA
Rajilic-Stojanovic et al 114	IBS (n=62) Ctrls (n=42)	Faeces	Phylogenetic 16S rRNA microarray and qPCR	IBS	↑ Proteobacteria and specific Firmicutes ↓ Other Firmicutes, Bacteroidetes and bifidobacteria	Finland
Carroll et al 115	IBS-D (n=16) Ctrls (n=21)	FaecesColonic mucosa	T-RFLP fingerprinting of 16S rRNA - PCR	IBS-D	Diminished microbial biodiversity in faecal samples	USA
Parkes et al 116	IBS-D (n=27) IBS-C (n=26) Ctrls (n=26)	Colonic mucosa	FISH Confocal microscopy	IBS	Expansion of mucosa-associated microbiota; mainly bacteroides and clostridia; association with IBS subgroups and symptoms	UK
Jeffery et al 117	IBS (n=37) Ctrls (n=20)	Faeces	Pyrosequencing 16SrRNA		Clustering of IBS patients—normal-like versus abnormal microbiota composition (increased ratio of Firmicutes to Bacteroidetes); association with symptom profile	Sweden

n, number of randomised subjects.
B, Bifidobacterium; C, constipation; C, Clostridium; Cl, Clostridium; ctrls, controls; D, diarrhoea; DGGE, denaturing gradient gel electrophoresis; FISH, fluorescent in situ hybridisation; IBS, irritable bowel syndrome; L, Lactobacillus; qPCR, quantitative PCR;R, Ruminococcus; S, Staphylococcus; T-RFLP, terminal restriction fragment length polymorphism.