1 Supplementary information A B Control Vitiligo-NL Vitiligo-L Control Vitiligo-NL Vitiligo-L phylum genus Alphaproteobacteria Paracoccus Gammaproteobacteria Acinetobacter Deltaproteobacteria Haematobacter Brevundimonas Pararhizobium Enhydrobacter Uncultured E. Shigella Roseomonas Amaricoccus Methylobacterium Rhodobacteraceae Sphingomonas Aureimonas Undibacterium Luteimonas Haemophilus Moraxella Ochrobactrum Pseudomonas Acetobacter 2 3 4 SUPPLEMENTARY FIGURE 1 Enrichment of Gammaproteobacteria and Paracoccus in 5 skin swab samples from vitiligo patients 6 Composition and relative abundance of Proteobacteria between different groups was examined 7 at phylum (A) and genus (B) levels. Individual subjects are shown as taxa bar plots (above) and 8 grouped data as pie charts (below). A complete list of OTUs is shown in Supplementary Table 9 5. 10 1 11 12 13 SUPPLEMENTARY FIGURE 2 Differences in b-diversity between swab and biopsy samples 14 PCoA plot representing b-diversity between biopsy and swab samples from the lesional and 15 non-lesional sites of vitiligo patients compared to healthy controls. Microbiota profile in skin 16 biopsies is very different from skin swabs (P<0.001) and skin biopsies taken from lesional sites 17 of vitiligo patients (light green) are significantly different from all other samples (P<0.001). 18 19 20 21 22 23 24 25 2 Control Vitiligo NL Vitiligo L Staphylococcus Cutibacterium Mycoplasma Streptococcus Mitochondrial DNA Corynebacterium Intestinibacteria Bacteroides Clostridium Enterococcus Escherichia-Shigella Parabacteroides Veillonella Bifidobacterium Gemella Rothia Raistonia Undibacterium Uncultured bacteria Lactobacillus 26 27 28 SUPPLEMENTARY FIGURE 3 Composition and diversity of skin microbiota in healthy and 29 vitiligo skin biopsy samples 30 Individual subject data are shown at the genus level in form of a heat map, illustrating the top 31 20 of the most abundant bacterial taxa between the three groups (n=10 per group). Differences 32 in microbial composition is tested using analysis of composition of microbiomes (ANCOM). 33 34 3 SUPPLEMENTARY TABLE 1 Stool OTUs in Figure 1 Complete list of OTUs in stool samples at phylum level SUPPLEMENTARY TABLE 2 Stool OTUs in Figure 1 Complete list of OTUs in stool samples at genus level SUPPLEMENTARY TABLE 3 Skin swab OTUs in Figure 3 Complete list of OTUs in swab samples at phylum level SUPPLEMENTARY TABLE 4 Skin swab OTUs in Figure 3 Complete list of OTUs in swab samples at genus level SUPPLEMENTARY TABLE 5 Proteobacteria OTUs in Supplementary Figure 1 Complete list of OTUs in biopsy samples from Proteobacteria family at phylum (top) and genus (bottom) level SUPPLEMENTARY TABLE 6 Skin Biopsy OTUs in Figure 4 Complete list of OTUs in biopsy samples at phylum level SUPPLEMENTARY TABLE 7 Skin Biopsy OTUs in Figure 4 Complete list of OTUs in biopsy samples at genus level 1 SUPPLEMENTARY TABLE 8 Sequences of fused primers 2 Forward: 3 AATGATACGGCGACCACCGAGATCTACACGTGCTAATAGGTTATGGTAATTAGCC 4 TACGGGNGGCWGCAGAATGATACGGCGACCACCGAGATCTACACGCGATCACAC 5 CTTATGGTAATTAGCCTACGGGNGGCWGCAGAATGATACGGCGACCACCGAGAT 6 CTACACAATGGACCGTTCTATGGTAATTAGCCTACGGGNGGCWGCAGAATGATA 7 CGGCGACCACCGAGATCTACACGTACGTCACTGATATGGTAATTAGCCTACGGGN 8 GGCWGCAGAATGATACGGCGACCACCGAGATCTACACTAGCCTGTCGTGTATGG 9 TAATTAGCCTACGGGNGGCWGCAGAATGATACGGCGACCACCGAGATCTACACA 10 CAGACGACGGATATGGTAATTAGCCTACGGGNGGCWGCAGAATGATACGGCGAC 11 CACCGAGATCTACACTCTATGCGAACGTATGGTAATTAGCCTACGGGNGGCWGC 12 AGAATGATACGGCGACCACCGAGATCTACACCTATGAGTCCAGTATGGTAATTAG 13 CCTACGGGNGGCWGCAGAATGATACGGCGACCACCGAGATCTACACGGAAACA 14 AACGGTATGGTAATTAGCCTACGGGNGGCWGCAGAATGATACGGCGACCACCGA 15 GATCTACACGATTGGCATAGTTATGGTAATTAGCCTACGGGNGGCWGCAGAATG 16 ATACGGCGACCACCGAGATCTACACGAGTTGTACGATTATGGTAATTAGCCTACG 17 GGNGGCWGCAGAATGATACGGCGACCACCGAGATCTACACCTCGAAATGCAATA 18 TGGTAATTAGCCTACGGGNGGCWGCAGAATGATACGGCGACCACCGAGATCTAC 19 ACAGAAGAAAGGCATATGGTAATTAGCCTACGGGNGGCWGCAGAATGATACGG 20 CGACCACCGAGATCTACACCCACTCTCTCTATATGGTAATTAGCCTACGGGNGGC 21 WGCAGAATGATACGGCGACCACCGAGATCTACACCCTCCTAATTCATATGGTAAT 22 TAGCCTACGGGNGGCWGCAGAATGATACGGCGACCACCGAGATCTACACTTCAT 23 GGCCAGCTATGGTAATTAGCCTACGGGNGGCWGCAG 24 25 Reversed: 26 CAAGCAGAAGACGGCATACGAGATTCAGTTCTCGTTAGTCAGTCAGCCGACTACH 27 VGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATTCGTGCGTGTTGAGTCA 28 GTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATGT 29 TATCGCATGGAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGA 30 CGGCATACGAGATGATCACGAGAGGAGTCAGTCAGCCGACTACHVGGGTATCTA 31 ATCCCAAGCAGAAGACGGCATACGAGATGTAAATTCAGGCAGTCAGTCAGCCGA 32 CTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATAGTGTTTCGGA 33 CAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACG 34 AGATACACGCGGTTTAAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCA 35 GAAGACGGCATACGAGATTGGCAAATCTAGAGTCAGTCAGCCGACTACHVGGGT 36 ATCTAATCCCAAGCAGAAGACGGCATACGAGATCACCTTACCTTAAGTCAGTCAG 37 CCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATTTAACCTT 38 CCTGAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCAT 39 ACGAGATTGCCGTATGCCAAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAA 40 GCAGAAGACGGCATACGAGATCGTGACAATAGTAGTCAGTCAGCCGACTACHVG 41 GGTATCTAATCCCAAGCAGAAGACGGCATACGAGATCGCTACAACTCGAGTCAG 42 TCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATTTA 43 AGACAGTCGAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGAC 44 GGCATACGAGATTCTGCACTGAGCAGTCAGTCAGCCGACTACHVGGGTATCTAAT 45 CCCAAGCAGAAGACGGCATACGAGATCGCAGATTAGTAAGTCAGTCAGCCGACT 46 ACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATCGGATAACCTCCA 47 GTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAG 48 ATAGGGTGACTTTAAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGA 1 49 AGACGGCATACGAGATGACTTCATGCGAAGTCAGTCAGCCGACTACHVGGGTAT 50 CTAATCCCAAGCAGAAGACGGCATACGAGATGCCTGTCTGCAAAGTCAGTCAGC 51 CGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCATACGAGATACTGATGG 52 CCTCAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAAGCAGAAGACGGCAT 53 ACGAGATTTCGATGCCGCAAGTCAGTCAGCCGACTACHVGGGTATCTAATCCCAA 54 GCAGAAGACGGCATACGAGATTGTGGCTCGTGTAGTCAGTCAGCCGACTACHVG 55 GGTATCTAATCCCAAGCAGAAGACGGCATACGAGATAACTTTCAGGAGAGTCAG 56 TCAGCCGACTACHVGGGTATCTAATCC 57 2 .