Fig. 6

Host genetic factors associated with the esophageal microbiome. a Host SNPs identified using MicrobiomeGWAS to be correlated with the Bray–Curtis resemblance matrix generated from square root-transformed species relative abundances (taxonomy arising from MetaPhlan2). Human SNPs were identified using the GATK toolkit onto the shotgun sequencing reads (depth of coverage (dp) = 2; minimum number of samples = 50). Blue line represents P = 0.1 and red line represents P = 0.05; all SNPs above the red line have significant P values. A complete list of SNPs across different thresholds is provided in Additional file 4.1–3. SNPs associated with microbiome composition mapped across most human chromosomes suggesting the analysis was not biased by low depth of coverage of the human genome. b PERMANOVA on Bray–Curtis resemblance matrix generated from square root-transformed species relative abundances (taxonomy arising from MetaPhlan2). Tests were applied across allele and genotype frequencies for human SNPs validated using Fluidigm custom SNPtype assays. A table of the genotyping results generated from the Fluidigm custom assays is provided in Additional file 4.4 and 5