Comparison-of-Small-Gut-and-Whole-Gut-Microbiota-of-First-Degree-Relatives-with-Adult-Celiac-Disease
Microbial diversity and composition analysis was done using the R-package phyloseq (v1.22.3) (McMurdie and Holmes, 2013) and microbiome R package (v1.0.2) (Leo and Shetty, 2017). To test for similarities in bacterial communities between sample types and diagnosis groups Analysis of Similarities (ANOSIM) on Bray-Curtis distances was used. ANOSIM function in vegan package (v 2.4-4) to calculate significance of PCoA clustering based on the Bray-Curtis distances (Dixon, 2003). To identify differentially abundant ASVs in pairwise comparisons between diagnosis groups we used DESeq2 (v1.18.0) (Love et al., 2014). All ASVs that were significantly (alpha = 0.01) different in abundance between the diagnosis groups were reported and were adjusted for multiple comparisons using the Benjamini-Hochberg, false discovery rate procedure. Data was visualized using ggplot2 (v 2.2.1) in R (Hadley Wickham, 2016).