Celiac Disease and a Gluten-Free Diet Lead to Loss of Methanobrevibacter from the Gut Microbiome

Abstract

Introduction: The importance of the human microbiome has become well known in recent years. The microbiome contains a diverse number of organisms including bacteria, archaea, fungi, and protozoa, which when imbalanced, can lead to a variety of dysbioses. Celiac disease (CD) is a condition where the immune system responds to gluten, a protein found in wheat, leading to chronic inflammation in the small intestine. Studies have found that microbial dysbiosis is often associated with patients who have CD, but few have looked at how gluten affects the microbiome in comparison to CD. This research sought to identify microbiome changes between people with CD (on a gluten-free diet), those on a gluten-free diet (without CD), and a control group (without CD and a gluten-free diet). Methods: Twenty-nine eligible participants (screened via a survey) provided a single stool sample (12 CD, 8 gluten-free, and 9 control). The microbial DNA was extracted from the stool samples using the QIAamp PowerFecal DNA Kit (Qiagen) and the V3/V4 region of 16s RNA using the 600-cycleMiSeq kit (Illumina). Sequenced DNA was sent to the University of Utah for analysis. Changes in microbiome diversity were statistically analyzed using a Kruskal-Wallis analysis. Results: No change in alpha or beta diversity was seen between any study groups. In addition, significance was not observed in common phyla normally affected by CD (Firmicutes, Bacteroides, and Actinobacteria). However, a statistically significant difference was seen in the archaeal genera Methanobrevibacter, which was found only in the control group (p = 0.0212). Discussion: Previously reported changes in the microbiome of CD patients were not observed in this study. However, changes could be seen in the archaeal genius, Methanobrevibacter, which was found only control group at an abundance of 3.3%. Thus, when CD individuals were compared to healthy individuals with similar gluten-free diets there was little difference in gut microbial species suggesting that gluten-free diet may normalize CD-related microbiome changes. Conclusion: The absence of Methanobrevibacter from CD and gluten-free groups requires additional analysis to understand what role Methanobrevibacter plays in the microbiome and how a gluten-free diet may affect that role.