Colgan, J. J. | bioRxiv Science

bioRxiv2022

Revaluation of old data with new techniques reveals novel insights into the celiac microbiome

Celiac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein expressed by wheat and other cereals, elicits an immune response leading to villous atrophy. Despite a strong genetic component, the disease arises sporadically throughout life, leading us to hypothesize the the microbiome might be a trigger for celiac disease. Here, we took microbiome data from 3 prior studies examining celiac disease and the microbiome and analyzed this data with newer computational tools and databases: the dada2 and PICRUSt2 pipelines and the SILVA database. Our results both confirmed findings of previous studies and generated new data regarding the celiac microbiome of India and Mexico. Our results showed that, while some aspects of prior reports are robust, older datasets must be reanalyzed with new tools to ascertain which findings remain accurate while also uncovering new findings. IMPORTANCEBioinformatics is a rapidly developing field, with new computational tools released yearly. It is thus important to revisit results generated using older tools to determine whether they are also revealed by currently available technology. Celiac disease is an autoimmune disorder that affects up to 2% of the worlds population. While the ultimate cause of celiac disease is unknown, many researchers hypothesize that changes to the intestinal microbiome play a role in the diseases progression. Here, we have re-analyzed 16S rRNA data from several previous celiac studies to determine whether previous results are also uncovered using new computational tools.

bioinformatics↗

bioRxiv2022

Celiac dysbiosis does not transcend geographic boundaries

Celiac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein found in wheat and other cereals, elicits an immune response that leads to villous atrophy. Despite a strong genetic component, celiac disease arises sporadically and at any age, leading us to hypothesize that changes in the microbiome influence celiac disease development and/or progression. Here, we pooled and computationally analyzed 16S data from 3 prior international studies that examined celiac disease and the microbiome. For our analysis, we combined the dada2 and PICRUSt 2 pipelines and a variety of data transformations that control for batch effects to determine whether any taxonomic or metabolic features were consistently associated with the celiac microbiome across the globe. Our results showed the celiac microbiome displays dysbiosis without a discernable pattern, which suggests perturbations in the celiac microbiome are a result of the disease rather than a cause. Data from PICRUSt 2 supported this conclusion and revealed connections between celiac disease and the metabolome that are supported by previous research examining dysbiotic microbiomes. IMPORTANCECeliac disease is an autoimmune disorder that affects roughly 2% of the worlds population. Although the ultimate cause of celiac disease is unknown, many researchers hypothesize that changes to the intestinal microbiome play a key role in disease progression. If this is the case, it may be possible to design therapies that manipulate the microbiome to suppress celiac disease. Here, we analyzed pooled data from 3 different studies from across the globe that examined celiac disease and the microbiome to ascertain whether there exists a unique celiac microbiome that transcends geographic boundaries.

bioinformatics↗