Gastroenterology

Gastroenterology

Volume 163, Issue 5, November 2022, Pages 1351-1363.e15
Gastroenterology

Original Research
Full Report: Gut Microbiota
Biogeographic Variation and Functional Pathways of the Gut Microbiota in Celiac Disease

https://doi.org/10.1053/j.gastro.2022.06.088Get rights and content

Background & Aims

Genes and gluten are necessary but insufficient to cause celiac disease (CeD). Altered gut microbiota has been implicated as an additional risk factor. Variability in sampling site may confound interpretation and mechanistic insight, as CeD primarily affects the small intestine. Thus, we characterized CeD microbiota along the duodenum and in feces and verified functional impact in gnotobiotic mice.

Methods

We used 16S rRNA gene sequencing (Illumina) and predicted gene function (PICRUSt2) in duodenal biopsies (D1, D2 and D3), aspirates, and stool from patients with active CeD and controls. CeD alleles were determined in consented participants. A subset of duodenal samples stratified according to similar CeD risk genotypes (controls DQ2–/– or DQ2+/– and CeD DQ2+/–) were used for further analysis and to colonize germ-free mice for gluten metabolism studies.

Results

Microbiota composition and predicted function in CeD was largely determined by intestinal location. In the duodenum, but not stool, there was higher abundance of Escherichia coli (D1), Prevotella salivae (D2), and Neisseria (D3) in CeD vs controls. Predicted bacterial protease and peptidase genes were altered in CeD and impaired gluten degradation was detected only in mice colonized with CeD microbiota.

Conclusions

Our results showed luminal and mucosal microbial niches along the gut in CeD. We identified novel microbial proteolytic pathways involved in gluten detoxification that are impaired in CeD but not in controls carrying DQ2, suggesting an association with active duodenal inflammation. Sampling site should be considered a confounding factor in microbiome studies in CeD.

Section snippets

Study Design and Patient Population

Adult patients attending the McMaster University Celiac Disease Clinic with an indication to undergo an upper gastrointestinal endoscopy were recruited for this study. CeD diagnosis (N = 24) was based on a positive transglutaminase-2 (TG2) test using the QUANTA Lite R h-tTG IgA enzyme-linked immunosorbent assay (Inova Diagnostics) or, in the case of IgA deficiency, with IgG deamidated gliadin peptide antibodies (Inova Diagnostics) and confirmed by means of duodenal biopsies assessed by a

Sampling Location Is a Key Determinant of Microbiota Composition in Celiac Disease

Microbiota composition was analyzed in duodenal aspirates, duodenal biopsies, and feces from patients with CeD and controls (Figure 1 and Supplementary Figure 1). Unsupervised hierarchical clustering according to sample location revealed gut location as a key determinant of microbiota composition (Figure 1A). This result was supported by β-diversity (weighted UniFrac) analysis, which showed distinct microbiota clustering by sample location (P = .001, R2 = 0.41) (Figure 1B). Permutational

Discussion

The past decades in microbiome research have significantly increased our understanding of microbial influence in CeD risk.41,43 However, as with other complex gastrointestinal conditions,44,45 universal microbiota signatures for CeD have not been found, due in part to the different methodological approaches and sampling site used.20,41 Indeed, most studies have relied on fecal samples, and none have directly compared, in the same population, microbial community differences between feces and

CRediT Authorship Contributions

Marco Constante, PhD (Data curation: Equal; Formal analysis: Equal; Investigation: Equal; Methodology: Equal; Software: Equal; Visualization: Equal; Writing – original draft: Equal).

Josie Libertucci, PhD (Data curation: Equal; Formal analysis: Equal; Investigation: Equal; Methodology: Equal; Software: Equal; Visualization: Equal; Writing – original draft: Equal).

Heather J. Galipeau, PhD (Investigation: Supporting; Resources: Supporting; Visualization: Supporting; Writing – review & editing:

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    Data Availability All sequencing data have been deposited in the Sequence Read Archive. The 16S rRNA gene sequencing data from human feces, duodenal aspirates, and biopsy samples (D1, D2, and D3) from patients with celiac disease and controls used in this study can be accessed under BioProject ID PRJNA812940.

    Author names in bold designate shared co-first authorship.

    Conflicts of interest The authors disclose no conflicts.

    Funding This study was funded by a Canadian Institutes of Health Research (CIHR) PJT-168840 awarded to Elena F. Verdu, who also holds a Canada Research Chair (CIHR) Tier 1 in Microbial Therapeutics and Nutrition in Gastroenterology. Josie Libertucci is funded by an IMAGINE-CIHR-Canadian Association of Gastroenterology postdoctoral research fellowship. Maria Ines Pinto-Sanchez research time is supported by an Alternate Funding Plan-Hamilton Academic Health Sciences Organization. Michael G. Surette holds a Canada Research Chair in Interdisciplinary Microbiome Research. PB holds the Richard Hunt-AstraZeneca Chair in Gastroenterology. Alberto Caminero holds a Paul Douglas Chair in Intestinal Research.

    Authors share co-first authorship.

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