A Metabolomic Perspective on Coeliac Disease

Table 1

Most relevant findings, and associated references, for studies linking gut microbiota and CD.

References	Type of sample	Technique	Microbiota phylum/class	Relevant findings
Wacklin et al. (2013) [55]	Mucosa biopsy	PCR-DGGE (real-time polymerase chain reaction, denaturing gradient gel electrophoresis), 16S rRNA sequencing	Firmicutes Bacteroides Proteobacteria Actinobacteria	Diversity in mucosal microbiota of celiac disease patients is associated with the symptoms of the disease.
Nistal et al. (2012) [57]	Duodenal biopsies	PCR (polymerase chain reaction)	Firmicutes Proteobacteria Bacteroidetes; Actinobacteria; Fusobacteria	Composition of small intestinal microbiota is similar between adults and children; there is higher number of Streptococcus and Prevotella in healthy subjects.
Nadal et al. (2007) [58]	Duodenal biopsy	FISH (Fluorescent in situ hybridization), Flow cytometry detection.		In faeces and duodenum of CD children, smaller amount of harmless bacteria (Lactobacillus and Bifidobacterium) and higher number of harmful bacteria are found (Bacteroides/Prevotella + E. coli) compared to healthy children.
Sánchez et al. (2010) [59]	Duodenal biopsy	PCR-DGGE	Bacteroidetes	Reduced number of intestinal microbiota in CD children but also in treated CD children was noticed. Treatment with GFD does not restore the bacteria composition.
Sánchez et al. (2011) [60]	Faeces samples	PCR-DGGE		Studies were carried out on stools of infants with high/low risk of CD and different types of milk feeding. High-risk infants have higher prevalence of Bacteroides vulgatus, whereas low-risk infants have higher population of B. uniformis, B. ovatus, and B. plebeius considering the subgroup of either breast-fed or formula-fed infants.
Cheng et al. (2013) [61]	Duodenal biopsy	qRT-PCR (quantitative real-time PCR)	Bacilli Bacteroides; Clostridium; Proteobacteria	Overall microbiota composition in the duodenal mucosa is comparable between healthy and CD children, but studied groups differ regarding bacteria subpopulation profile.
Sellitto et al. (2012) [51]	Faeces samples	qPCR (quantitative PCR)	Bacteroidetes; Firmicutes	Lack of microflora maturation during first 2 years of life in infants at risk of CD. Moreover, there was observed absence of Bacteroidetes and abundance of Firmicutes.
Sanz et al. (2007) [54]	Faeces samples	PCR-DGGE	Actinobacteria; Firmicutes	Lactobacillus and Weissella are more abundant and diverse in treated CD patients and control subjects than in active CD individuals. Composition of lactic bacteria and Bifidobacterium differs between celiac children and age-matched controls.
Kaufman and Rousseeuw (2009) [62]	Intestine biopsies	PCR	Proteobacteria	There observed no statistical differences in bacteria composition between healthy and CD children. Nevertheless,   Haemophilus was more common in CD patients and Neisseria  polysaccharea in control individuals.
di Cagno et al. (2011) [63]	Faeces sample, duodenal biopsy	RAPD (random amplification of polymorphic DNA) -PCR	Eubacteria	Higher number of different Eubacteria classes was found in duodenum of coeliac children under gluten-free diet than in healthy children.
Medina et al. (2008) [64]	Faeces sample	PBMC (peripheral blood mononuclear cell) phenotyping and flow cytometric analyses	Actinobacteria	Studies regarding interaction between faecal bacteria and immune system response of coeliac disease patients. It appeared that Gram-positive bacteria such as Lactobacillus and Bifidobacterium may act as inhibitors of inflammation.