Table 3

Summary of culture and molecular studies of colonic microbiome

StudySubjectSampleMethodPatient groupMain findingCountry of study
Balsari et al 96
  • IBS (n=20) Ctrls (n=20)

FaecesCultureIBS
  • ↓ Coliform bacteria

  • Lactobacillus spp.

  • Bifidobacterium spp.

Italy
Si et al 98
  • IBS (n=25) Ctrls (n=25)

FaecesCultureIBS
  • ↓ Bifidobacterium

  • ↑ Enterobacteriaceae

  • C perfringens

China
Malinen et al 99
  • IBS (n=27) Ctrls (n=22)

FaecesqPCRIBS
  • 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)

FaecesCulturePCR-DGGEIBS
  • ↑ 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)

FaecesMicroarrayIBS
  • 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)

FaecesGC-profiling + sequencing of 16S rRNA genesIBS-D
  • ↑ Proteobacteria

  • ↑ Firmicutes

  • ↓ Actinobacteria

  • ↓ Bacteroidetes

Finland
Lyra et al 106
  • IBS (n=20) Ctrls (n=15)

FaecesqPCRIBS-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-DGGEIBS
  • ↑ 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)

FaecesPCR-DGGE + sequencing of 16S rRNA genesIBS
  • ↓ Bacterial species

  • ↓ Biodiversity

  • ↑ Biological variability of predominant bacteria

UK
Malinen et al 110
  • IBS (n=44)

FaecesqPCR
  • R torques 94% symptom severity

  • Other phylotypes neg assoc.

Finland
Ponnusamy et al 111
  • IBS (n=11) Ctrls (n=8)

FaecesDGGE + qPCR of 16sRNA genes
  • ↑ Diversity in Bacteroidetes & Lactobacilli

  • ↑ Alanine & pyroglutamic acid & phenolic compounds

Korea
Rinttila et al 112
  • IBS (n=96) Ctrls (n=23)

FaecesqPCRIBS
  • S aureus (17%)

Finland
Saulnier et al 113
  • IBS (n=22) Ctrls (n=22) (Children)

Faeces16s Metagenomic sequencing and DNA microarrayIBS
  • ↑ γ Proteobacteria

  • Classified IBS subtypes using sets of discriminant bacterial species

USA
Rajilic-Stojanovic et al 114
  • IBS (n=62) Ctrls (n=42)

FaecesPhylogenetic 16S rRNA microarray and qPCRIBS
  • ↑ Proteobacteria and specific Firmicutes

  • ↓ Other Firmicutes, Bacteroidetes and bifidobacteria

Finland
Carroll et al 115
  • IBS-D (n=16) Ctrls (n=21)

FaecesColonic mucosaT-RFLP fingerprinting of 16S rRNA - PCRIBS-DDiminished microbial biodiversity in faecal samplesUSA
Parkes et al 116
  • IBS-D (n=27) IBS-C (n=26) Ctrls (n=26)

Colonic mucosa
  • FISH

  • Confocal microscopy

IBSExpansion of mucosa-associated microbiota; mainly bacteroides and clostridia; association with IBS subgroups and symptomsUK
Jeffery et al 117
  • IBS (n=37) Ctrls (n=20)

FaecesPyrosequencing 16SrRNA Clustering of IBS patients—normal-like versus abnormal microbiota composition (increased ratio of Firmicutes to Bacteroidetes); association with symptom profileSweden
  • 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.