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Supplemental Figures and Legends.Pdf Supplemental Figures and Tables Supplemental Tables Table S1. Per-patient characteristics and summary Table S2. Correlations between relative abundances calculated from 454 vs Sanger amplicon sequencing Table S3. Summary of rarefaction analysis, subsampled Table S4. Summary of patient treatments Table S5. Shannon diversity indices and statistical testing on subsampled (n=100) data, by treatment effect Table S6. Sample sizes for analysis Table S7. Shannon diversity indices and statistical testing on subsampled (n=100) data Table S8. Theta similarity indices and statistical testing for subsampled (n=100) values Table S9. Genera significantly over/underrepresented (adjusted P-value < 0.1) between groups, all sites Table S10. Staphylococcal species significantly over/underrepresented between groups, all sites Table S11. Spearman correlation between taxonomic abundance (Af) and patient clinical metadata Table S12. Fungal-based analysis of select individuals Table S13. Order of subjects in relative abundance plots in Fig. 2, 6, S4, S7 Table S14. Random forests analysis of bacterial taxa. Supplemental Figures Figure S1. Partial Spearman correlation () between samples sequenced by Sanger vs. 454. Colors indicate patient category; plots are separated by taxonomy. Most abundant taxonomies are shown. Table (bottom right) shows the partial correlation for each taxa, adjusting for patient, and associated P-value. Figure S2. Rarefaction analysis for the skin and nares microbiota sampling at each site (antecubital fossa (Af), retroauricular crease (Ra), nares (N), popliteal fossa (Pf), volar forearm (Vf)) calculated as operational taxonomic units (OTUs) at a cutoff of 97% similarity. Sanger samples are shown in (A); 454 samples are shown in (B). Each point represents mean ± SEM of all individuals at specified site and patient category. Figure S3. The effect of treatment on community diversity. Treatments assessed were whether the patient (STAT3-HIES, DOCK8, or WAS; represented as different shapes) had taken antibiotics or steroids orally within the last month or topically within the last seven days (“recent treatment”, light blue) versus greater than one month or seven days, respectively (“no recent treatment”, dark blue). Each point represents the value for an individual patient timepoint, separated by site. Figure S4. Additional bacterial taxonomic classifications for the (A) antecubital fossa, (B) nares, (C) retroauricular crease, and (D) volar forearm. Relative abundances of 14 major phyla-family taxonomies (top) are shown grouped by patient category. On the bottom are relative abundances of species-level classification of staphylococcal and streptococcal species. Order of subjects follows the top; full subject information is shown in Table S13. Figure S5. Barplots of mean proportions (± SEM) of select significantly different major genera/species in the antecubital fossa by patient category, as represented by piecharts in Fig. 2 and Fig. 5. Figure S6. Additional principal coordinates analysis (PCoA) plots of the Yue-Clayton theta coefficient showing taxonomies associated with variation within and between individuals. Description follows from Fig. 3. Biplot arrows indicate the most significant unique consensus taxonomies contributing to variation along axis 1; Spearman correlations () are with axis 1. Length of biplot arrows reflects the contribution of that taxa to the top three axes. Associated P- values < 2.2x10-16. % variation attributed to an axis is indicated. N nares; Vf volar forearm. Figure S7. Heatmap of mean Theta similarity coefficients of pairwise comparisons of communities within or between different patient groups. Darker color indicates higher similarity: θ=0 indicates that two samples have no species in common and θ=1 indicates that two samples are identical. N.D. indicates no data available. Figure S8. Additional fungal taxonomic classifications for the (A) antecubital fossa, (B) nares, (C) retroauricular crease, and (D) volar forearm, grouped by patient category. Description follows from Fig. 6B. ! Figure S9. Correlations of relative abundances of fungal and bacterial taxa at each site. Correlations were analyzed for fungal and bacterial genera, and when possible species, that occurred in >25% of either control or STAT3-HIES patient samples. Spearman correlations between relative abundances of fungal vs. bacterial phylotypes with mean abundance across samples > 0.25% were calculated for two-way unsupervised hierarchical clustering of the Spearman correlation coefficients. Reds indicate correlation; blues indicate anti-correlation. (A) Af, (B) N, (C) Ra, (D) Vf. Left, control heatmap; right, STAT3-HIES. ! ! ! Figure S1. Corynebacterium Actinobacteria (Other) Propionibacterium Bacteroidetes Clostridia 1.00 0.75 0.50 0.25 0.00 Firmicutes (Other) Staphylococcus aureus Staphylococcus capitis Staphylococcus epidermidids Staphylococcus (Other) 1.00 0.75 0.50 0.25 AD 0.00 CTRL Streptococcus Other Alphaproteobacteria Betaproteobacteria Gammaproteobacteria 1.00 HIES 0.75 WAS 0.50 Relative abundance, Sanger 0.25 0.00 Enterobacteriaceae Proteobacteria (Other) 1.00 Taxa P T P Corynebacterium 0.81 2.0E-70 Staphylococcus epidermidis 0.74 8.2E-45 0.75 Actinobacteria (other) 0.77 3.1E-52 Staphylococcus (other) 0.64 2.4E-26 Propionibacterium 0.87 9.9E-117 Streptococcus 0.72 1.7E-39 0.50 Bacteroidetes 0.73 1.5E-42 Other 0.50 2.2E-13 Clostridia 0.66 6.1E-30 0.61 8.4E-23 0.25 Beta 0.67 6.6E-31 Staphylococcus aureus 0.62 2.1E-24 Gamma 0.64 1.7E-26 0.00 Staphylococcus capitis 0.42 2.6E-09 Enterobacteriaceae 0.55 5.3E-17 0.00 0.25 0.50 0.75 1.00 0.25 0.50 0.75 1.00 (other) 0.47 1.4E-11 Relative abundance, 454 Figure S2. A Af N 60 ● ● 50 ● ● ● ● ● 40 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 30 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 20 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 10 ● ● ● ● ● ● ● ● ● ● ● TUs ● O 0 ● ● Ra Vf 60 ● ● ● ● ● Number of ● 50 ● ● ● ● ● 40 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 30 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 20 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 10 ● ● ● ● ● ● ● ● ● ● ● 0 ● ● AD ● CTRL 1 1 102030405060708090100110120130140150160170180190199 102030405060708090100110120130140150160170180190199 Number of sequences sampled ● DOCK8 ● HIES B Af N ● WAS 100 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 50 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● TUs O 0 ● ● Ra Vf ● ● ● Number of ● ● ● 100 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 50 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0 ● ● 1 1 100 200 300 400 500 600 700 800 900 1000 100 200 300 400 500 600 700 800 900 1000 Number of sequences sampled Figure S3. Antibiotic, oral Steroids, oral Topical, any Af Af Af 4 ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ● ●● ● ● ●● ● ● 3 ● ● ●● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● 2 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1 ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ● 0 N N N 4 ● ● ● ● ● ● ● ● ● 3 ●● ● ●● ● ●● ● ● ● ● x ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● e ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● 2 ●●● ● ● ● ● ● ●●● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ● ● ● ●● ●● ● ●●● ● ● ● ● ●● ●● ● ●●● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ●● ● ● ● ●● ● ● CTRL, no recent treatment ● ●● ● ● ● ●● ● ● ● ●● ● ● 1 ● ● ● ● ● ● HIES, no recent treatment 0 ersity Ind WAS, no recent treatment v Ra Ra Ra DOCK8, no recent treatment 4 3 HIES, yes recent treatment Shannon Di 2 WAS, yes recent treatment ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1 ● ●● ●●●● ● ● ●● ●●●● ● ● ●● ●●●● ● DOCK8, yes recent treatment ● ● ● ● ● ● ● ● ● ● ● ● ●●●●● ● ● ● ●●●●● ● ● ● ●●●●● ● ● ● ● ● ● ● ● ● 0 ● ● ● ● ● ● ● ● ● Vf Vf Vf ● ● ● ● ● ● ● ● ● 4 ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ●● ● ●● ●● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● 3 ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ●●●● ● ●●●● 2 ● ● ●● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ●● 1 ● ●● ● ●● ● ●● Figure S4A. A Control Atopic Dermatitis HIES WAS DOCK8 1.0 0.8 Actinobacteria Corynebacteriaceae Propionibacteriaceae Bacteroidetes 0.6 Firmicutes Staphylococcaceae ercentage Streptococcaceae Clostridia 0.4 Other Af, P Proteobacteria Alphaproteobacteria Betaproteobacteria 0.2 Gammaproteobacteria Enterobacteriaceae Serratia 0.0 1.0 Staph. aureus Staph. capitis Staph. epidermidis Staph. hominis 0.8 Staph. haemolyticus Staph. other Str. gordonii Str. pneumo 0.6 Str. salivaris Str. sanguinis Str. other ercentage Other 0.4 Af, P 0.2 0.0 Figure S4B. B Control Atopic Dermatitis HIES WAS DOCK8 1.0 0.8 Actinobacteria Corynebacteriaceae 0.6 Propionibacteriaceae Bacteroidetes Firmicutes ercentage Staphylococcaceae 0.4 Streptococcaceae N, P Clostridia Other Proteobacteria Alphaproteobacteria 0.2 Betaproteobacteria Gammaproteobacteria Enterobacteriaceae Serratia 0.0 1.0 Staph. aureus Staph. capitis Staph. epidermidis 0.8 Staph. hominis Staph. haemolyticus Staph. other Str. gordonii 0.6 Str. pneumo Str. salivaris Str. sanguinis ercentage Str. other 0.4 Other N, P 0.2 0.0 Figure S4C. C Control HIES WAS DOCK8 1.0 0.8 Actinobacteria Corynebacteriaceae Propionibacteriaceae 0.6 Bacteroidetes Firmicutes ercentage Staphylococcaceae Streptococcaceae 0.4 Clostridia Ra, P Other Proteobacteria Alphaproteobacteria 0.2 Betaproteobacteria Gammaproteobacteria
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