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. 2012 Jul 10;62(1):159–176. doi: 10.1136/gutjnl-2012-302167

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
IBS-C

  • ↓ Cl coccoides group
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.