Table 1.

Studies which have shown altered fecal and mucosal microbiome in disease states.

Group	Method, microbiota analyzed	Diagnostic criteria and subjects	Finding	Reference
IBS	Q-PCR, fecal microbiome	Rome II, n = 27	↓ Lactobacillus spp. in IBS-D subjects	Malinen et al. (2005)
		BS-D (n = 12), IBS-C (n = 9), IBS-A (n = 6)	↑ Veillonella spp. in IBS-C
	Culture/DGGE, fecal microbiome	Rome II, n = 26	Increased number of aerobes in IBS patients	Mättö et al. (2005)
		BS-D (n = 12), IBS-C (n = 9), IBS-A (n = 5)	Temporal instability in IBS patients revealed by DGGE
	Q-PCR, Phylogenic Microarray, fecal microbiome	Rome II, n = 62 IBS-D (n = 25), IBS-C (n = 18), IBS-A (n = 19)	↑ Ratio of the Firmicutes to Bacteroidetes in IBS	Rajilic-Stojanovic et al., 2011)
			↑ in numbers of Dorea, Ruminococcus, and Clostridium spp. in IBS
			↓ Bacteroidetes in IBS
			↓ Bifidobacterium and Faecalibacterium spp.
			↓ Average number of methanogens in IBS
	Fractionation/16S rRNA gene cloning and sequencing, Q-PCR, fecal microbiome	Rome II, n = 24	Significant differences in Coprococcus, Collinsella, and Coprobacillus Phyla in the IBS group compared to controls	Kassinen et al. (2007)
		IBS-D (n = 10), IBS-C (n = 8), IBS-A (n = 6)
	DGGE, fecal microbiome	Rome II, n = 47	Significant difference between IBS and healthy controls	Codling et al. (2010)
		No sub-typing	Significantly more variation in microbiota of healthy volunteers than that of IBS patients
	FISH, fecal and duodenal microbiome	Rome II, n = 41	↓ Bifidobacteria in IBS subjects compared to healthy controls	Kerckhoffs et al. (2009)
		IBS-D (n = 14) IBS-C (n = 11) IBS-A (n = 16)
	Q-PCR, fecal microbiome	Rome II and III, n = 26	↑ Veillonella and Lactobacillus in IBS	Tana et al. (2010)
		IBS-D (n = 8) IBS-C (n = 11) IBS-A (n = 7)
IBD	FISH adapted to flow cytometry, fecal microbiota	Active CD (n = 13)	Clostridium coccoides was reduced in UC	Sokol et al. (2006)
		Active UC (n = 13)	C. leptum group was reduced in CD
		IC (n = 5), HS (n = 13).	Bacteroides group was more abundant in IC
	16S rRNA DGGE analysis, fecal microbiota	Active CD (n = 5) Inactive CD (n = 11), HS (n = 18)	↓ Temporal stability of dominant species for all Crohn’s disease patients	Scanlan et al. (2006)
			Bifidobacterium spp. were similar in all samples
			Clostridiales and Bacteroidales communities are altered in Crohn’s disease
	DGGE, Q-PCR, fecal microbiota	CD (n = 68) Unaffected relatives (n = 84), HS (n = 55)	CD vs. unaffected relatives	Joossens et al. (2011)
			↓ Dialister invisus, an uncharacterized species of Clostridium cluster XIVa, Faecalibacterium prausnitzii and Bifidobacterium adolescentis
			↑ Ruminococcus gnavus
			Unaffected relatives vs. HS
			↓ Collinsella aerofaciens and member of the Escherichia coli–Shigella group
			↑ Ruminococcus torques
	T-RFLP analysis16S rRNA gene, Q-PCR, ileal and rectal biopsies	Monozygotic twin pairs that were discordant (n = 6) or concordant (n = 4) for CD, HS (n = 6)	Predominantly ileal CD vs. co-twins and CD localized in the colon	Willing et al. (2009)
			↓ Faecalibacterium prausnitzii
			↑ Escherichia coli
	16S rRNA gene sequencing, mucosal biopsies	Inflamed and non-inflamed intestinal tissue from 6 CD (n = 12), 6 UC (n = 12), HS (n = 5)	↓ Mucosal microbial diversity in IBD	Walker et al. (2011)
			↓ Firmicutes in IBD samples and ↑ Bacteroidetes
			↑ Enterobacteriaceae in CD only significant differences in microbial community structure between inflamed and non-inflamed mucosal sites
	rRNA sequence analysis and Q-PCR	UC (n = 61), CD (n = 68)	↓ Bacteroidetes and Lachnospiraceae in IBD	Frank et al. (2007)
		HS (n = 61)	↑ Actinobacteria and Proteobacteria in IBD
Obesity	Pyrosequencing, cecal contents	Ob/Ob mice	↑ Firmicutes	Turnbaugh et al. (2006)
			↓ Firmicute to Bacteroides ratio
	16S rRNA sequencing, cecal contents	Ob/Ob mice	↓ Bacteroidetesob/ob animals	Ley et al. (2005)
			↑ Firmicutes
	16S rRNA sequencing	Human	↓ Bacteroides in obesity	Ley et al. (2006b)
			↑ Bacteroides during calorie restriction
	Q-PCR, MALDI-TOF spectral analysis, fecal microbiota	Human	Bifidobacterium animalis and Methanobrevibacter smithii were associated with normal bodyweight	Million et al. (2011)
			Lactobacillus reuteri was associated with obesity
Autism	Q-PCR, fecal microbiota	Autistic (n = 15), HS (n = 8)	↑ Clostridium bolteae and Clostridium clusters I and XI in autistic children	Song et al. (2004)
			↓ Clostridium cluster XIVab in autistic children
	16S rRNA gene sequencing and culture, fecal microbiota Gastric and duodenal sampling	Autistic (n = 13), HS (n = 8)	Fecal samples	Finegold et al. (2002)
			Children with autism had nine species of Clostridium not found in controls
			Control children had three species of Clostridium not found in autistic children Gastric and duodenal Specimens
			No non-spore-forming anaerobes and microaerophilic bacteria from controls significant numbers of non-spore-forming anaerobes and microaerophilic bacteria in children with autism
	Pyrosequencing, fecal microbiota	Autistic (n = 33) Non-affected siblings (n = 7), HS (n = 8)	↑ Increased diversity and richness in the autistic gastrointestinal microbiome	Finegold et al. (2010)
			↑ Bacteroidetes in the severely autistic group
			↑ Firmicutes in the control group
			↑ Desulfovibrio species and Bacteroides vulgatus autistic children

IBS-D, diarrhea predominant IBS; IBS-C, constipation predominant IBS; IBS-A, alternating IBS; UC, ulcerative colitis; CD, Crohn’s disease; IC, infectious colitis; HS, healthy subjects; DGGE, denaturing gradient gel electrophoresis; Q-PCR, quantitative PCR; FISH, fluorescent in situ hybridization; T-RFLP, terminal restriction length polymorphism.