Unraveling the ties between irritable bowel syndrome and intestinal microbiota

Table 1 Summary of molecular studies of intestinal microbiota in irritable bowel syndrome

Ref.	Ethnicity	IBS patients, n	Mean age (range), yr	Male gender, n	IBS subtype			Controls, n	Sample	Method	Changes in intestinal microbiota composition in IBS
					IBS-C	IBS-D	IBS-M
Malinen et al[83] 2005	Finland	27	46.5 (20-65)	7	9	12	6	22 (age, gender matching)	Feces	qPCR covering bacteria 300 bacterial species	IBS-D: ↓ lactobacillus spp.
											IBS-C: ↑ veillonella spp.
											Overall IBS: ↓ clostridium coccoides subgroup, Bifidobacterium catenulatum group
Mättö et al[46] 2005	Finland	26	46 (20-65)	7	9	12	5	25 (age, gender matching)	Feces	Culture, PCR-DGGE	Temporal instability in the bacterial population↑ coliform bacteria
											↑ aerob:anaerob ratio
Maukonen et al[84] 2006	Finland	24	45 (24–64)	5	6	7	3	16	Feces	PCR-DGGE, Transcript analysis with the aid of affinity capture for Clostridial groups	Temporal instability in the bacterial population
											IBS-C: ↓ clostridium coccoides-Eubacterium rectale group
Kassinen et al[43] 2007	Finland	24	47.3 (21–65)	5	8	10	6	23 (age, gender matching)	Feces	GC-profiling + high-throughput 16S rRNA gene sequencing of 3753 clones	Coverage of the clone libraries of
											IBS subtypes and control subjects differed
Kerckhoffs et al[85] 2009	The Netherlands	41	42 ± 2.12	12	11	11	16	26	Feces, Duodenal mucosa	FISH, qPCR	↓ bifidobacterium catenulatum
Krogius-Kurikka et al[86] 2009	Finland	10	46.5	4	0	10	0	22	Feces	G + C (%G + C) -based profiling and fractioning combined with 16S rRNA gene clone library sequencing of 3267 clones	↑ proteobacteria
											↑ firmicutes
											↓ actinobacteria
											↓ bacteroidetes
Lyra et al[87] 2009	Finland	20	IBS-D: 43.6 (26-60), IBS-C: 48.6 (24-64), IBS-M: 50.8 (31-62)	6	8	8	4	15	Feces	qPCR	IBS-D: ↑ ruminococcus torques, ↓ clostridium thermosuccinogenes
											IBS-C: ↑ ruminococcus bromii-like
											IBS-M: ↓ ruminococcus torques, ↑ clostridium thermosuccinogenes
Tana et al[88] 2010	Japan	26	21.7 ± 2.0	13	11	8	7	26 (age, gender matching)	Feces	Culture, qPCR	↑ veillonella spp.
											↑ lactobacillus spp.
Codling et al[89] 2010	Ireland	47	43.6 (24–66)	0	-	-	-	33	Feces, Colonic mucosa	PCR-DGGE	Significantly more variation in the gut microbiota of healthy volunteers than that of IBS patients
Ponnusamy et al[90] 2011	South Korea	11	47.5 (18-74)	6	-	--		8	Feces	DGGE + qPCR of 16S rRNA genes	↑ diversity of Bacteroidetes and Lactobacillus groups
Rinttilä et al[91] 2011	Finland	96	47 (20-73)	27	15	81		23	Feces	qPCR	17% of IBS samples (n = 15) tested positive for staphylococcus aureus
Rajilić-Stojanović et al[45] 2011	Finland	62	49 (22−66)	5	18	25	19	42	Feces	Phylogenetic 16S rRNA microarray and qPCR	2-fold ↑ firmicutes:Bacteroidetes ratio↓ bacteroidetes, ↑ dorea, ruminococcus, clostridium sppBifidobacterium faecalibacterium spp
Carroll et al[51] 2011	United States	16	35.6 (23–52)	5	0	16	0	21	Feces, Colonic biopsies	T-RFLP fingerprinting of 16S rRNA-PCR	↓ microbial biodiversity in D-IBS fecal samples
Parkes et al[52] 2012	United Kingdom	53	IBS-D: 36.2 (32.1–40.3), IBS-C: 32.4 (28.1–36.7)	28	26	27	0	26	Colonic mucosa	FISH, confocal microscopy	Expansion of mucosa-associated microbiota; mainly bacteroides and clostridia; association with IBS subgroups and symptoms
Jeffery et al[92] 2012	Sweden	37	37 ± 12	11	10	15	12	20	Feces	Pyrosequencing 16SrRNA	Clustering of IBS patients: normal-like vs abnormal microbiota composition (increase of firmicutes-associated taxa and a depletion of bacteroidetes-related taxa)

IBS: Irritable bowel syndrome; IBS-D: Diarrhea-predominant irritable bowel syndrome; IBS-C: Constipation-dominant irritable bowel syndrome; IBS-M: Alternating type or mixed irritable bowel syndrome; PCR-DGGE: PCR denaturing gradient gel electrophoresis; FISH: Fluorescent in situ hybridization; qPCR: Quantitative PCR; 16S rRNA: 16S ribosomal RNA.

Table 2 Advantages and limitations of the principal techniques used in the characterization of the intestinal microbiota[16,39]

	Advantages	Limitations
Culture	Cheap, easy to use	Limited estimate intestinal microbiota
PCR-T/DGGE	High sensitivity in detecting difference in bacterial populations, semi-quantitative	Does not identify bacteria unless bands on the gel are cut out and sequenced
FISH	Microbial in situ identification, high sensitivity, quantitative	Few species can be simultaneously detected, only known species are detected
T-RFLP	Low cost	Low biodiversity resolution, no species-level identification, not quantitative
Quantitative PCR	Can detect small number of bacteria and quantify them	Laborious
Phylogenetic microarray	High biodiversity resolution, quantitative	Only known species are detected
NGS phylogenetic analysis (e.g., pyrosequencing)	Enormous quantities of data at individual Species level	Very costly, need bioinformatics analysis

16S rRNA: 16S ribosomal RNA; PCR-T/DGGE: PCR temperature/denaturing gradient gel electrophoresis; FISH: Fluorescent in situ hybridization; T-RFLP: Terminal restriction fragment length polymorphism; qPCR: Quantitative PCR; NGS: Next-generation sequencing.

Table 3 Systemic reviews for randomized controlled trials of probiotics in irritable bowel syndrome

Ref.	Selection criteria	n of identified studies	Results
McFarland et al[73] 2008	RCTs in humans published as full articles or meeting abstracts in peer-reviewed journals	20 RCTs	Global IBS symptoms: RR = 0.77 (95%CI: 0.62-0.94)/ abdominal pain: RR = 0.78 (95%CI: 0.69-0.88)
Brenner et al[76] 2009	RCTs; adults with IBS defined by Manning or Rome II criteria; single or combination probiotic vs placebo; improvement in IBS symptoms and/or decrease in frequency of adverse events reported	16 RCTs → 11 studies showed suboptimal study design	Bifidobacterium infantis 35624 has shown efficacy for improvement of IBS symptoms. Most RCTs about the utility of probiotics in IBS have not used an appropriate study design
Hoveyda et al[74] 2009	RCTs compared the effects of any probiotic therapy with placebo in patients with IBS	14 RCTs → 7 RCTs providing outcomes as dichotomous variable and 6 RCTs providing outcomes as continuous variable	Overall symptoms: dichtomous data - OR = 0.63 (95%CI: 0.45-0.83)/continuous data - mean ± SD, 0.23 (95%CI: 0.07-0.38) Trials varied in relation to the length of treatment (4-26 wk), dose, organisms and strengths of probiotics used
Moayyedi et al[75] 2010	RCTs comparing the effect of probiotics with placebo or no treatment in adult patients with IBS (over the age of 16 yr)	19 RCTs → 10 RCTs providing outcomes as a dichotomous variable	Probiotics appear to be efficacious in IBS (Probiotics were statistically significantly better than placebo, but there was statistically significant heterogeneity). The magnitude of benefit and the most effective species and strain are uncertain
Ortiz-Lucas et al[77] 2013	RCTs comparing probiotics with placebo in treating IBS symptoms	24 RCTs → 10 RCTs providing continuous data performed with continuous data summarized using mean ± SD and 95%CIs	Pain scores: improved by probiotics containing Bifidobacterium breve, Bifidobacterium longum, or Lactobacillus acidophilus species Distension scores: improved by probiotics containing B. breve, B. infantis, Lactobacillus casei, or Lactobacillus plantarum species Flatulence: improved by probiotics containing B. breve, B. infantis, L. casei, L. plantarum, B. longum, L. acidophilus, Lactobacillus bulgaricus, and Streptococcus salivarius ssp. thermophilus

IBS: Irritable bowel syndrome; RCT: Randomized controlled trial.