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 B N, Percentage N, Percentage Figure S4B. 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 Control Atopic Dermatitis HIES WAS DOCK8 Proteobacte Other Fi Bacteroidetes Actinobacte Gammaproteobacte Betaproteobacte Alphaproteobacte Clost Enterobacteriaceae r Other Str. other Str. sanguinis Str. sali Str. pneumo Str. gordonii Staph. other Staph. haemolyticus Staph. hominis Staph. epide Staph. capitis Staph. aureus micutes Streptococcaceae Stap Propionibacte Co Serratia r r idia ynebacte h v a ylococcaceae r is r r r midis ia ia r iaceae r r iaceae ia r ia r ia 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 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

ercentage Str. sanguinis Str. other 0.4 Other Ra, P

0.2 Figure S4D.

D Control Atopic Dermatitis HIES WAS DOCK8 1.0

0.8 Actinobacteria Corynebacteriaceae 0.6 Propionibacteriaceae Bacteroidetes Firmicutes

ercentage Staphylococcaceae Streptococcaceae 0.4 Vf, 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

ercentage Str. sanguinis Str. other 0.4 Other Vf, P

0.2

0.0 Figure S5.

CTRL WAS DOCK8 0.4 HIES tion

r AD e propo v

0.2 Mean relati

0.0

Stap Propionibacte Co S.epide S.haemolyticus rynebacte Anaerococcus hylococcus S.aureus Ser rmidis ratia rium rium Figure S6. Staphylococcus N ● ) ● ● ● ● ●●●● ● ●●●● ●● ●●●● ●●● ● ●● ● ●● ● ● ●● ● ●●● ● ● ● ● ●●● ● ● ● ● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● Corynebacterium ● ● ● ● ● ● ●● ) ●● ●● ●●● ● ●● ● ● ●● ● ● ●● ● ●● ● ● ● ● ● ●● ●●●●●● ● ●● ● ● ● ●● ● ●●●● Anaerococcus ●●● ●● ●●●● ● Streptococcus ●● ● ● ● ● ) )

PCoA axis 3 (6.6%) Propionibacterium )

● AD PCoA axis 1 (13.1%) ● CTRL ● DOCK8 ● HIES ● WAS Vf ● ● ● ●● ● ●●

● ●● ● ● ● ● ● ● ●● N, Neisseria ()

● ● ● ● ●● ●●● ● C, Corynebacterium ) ● ● ● ●● ● ●● ●●● ● ● ●● ● ● G, Gemella ) ● ●● ●●●●● ● ● ●●● ● ● ● ● A, Actinomyces ) ● ● ● ● ● ●● ● ● ●●●● ● ●●● ● ● ● ●● ● ● ●●● ● ●● ●● ●● ● ● ● ● ● ● ● ● ● ●● ● Streptococcus ● ● ● ● ● ● ● ●●● ● ●● ●● ● ● ●● ● ) ● ● ●●●● ● ● ●●● N C Propionibacterium G A ) Figure S7. 0 0.2 0.4 Theta

CTRL_CTRL N.D. AD_AD Within-group DOCK8_DOCK8 HIES_HIES WAS_WAS CTRL_DOCK8 N.D. AD_DOCK8 Vs. Controls CTRL_HIES N.D. AD_HIES CTRL_WAS N.D. AD_WAS HIES_DOCK8 Between PID HIES_WAS WAS_DOCK8 Af N Ra Vf Figure S8. Control HIES Ascomycota 1.0 Aureobasidium Dothioraceae Ascochyta 0.8 Phoma Aspergillus Podosphaera 0.6 Saccharomyces Saccharomycetaceae Basidiomycota 0.4 Gloeophylllum Malassezia globosa ercentage, Af restricta P 0.2 sympodialis Other 0.0 Rhodotorula 1.0 Cryptococcus Phylum incertae sedis Rhizopus 0.8 Other

0.6

0.4 ercentage, N

P 0.2

0.0 1.0

0.8

0.6

0.4 ercentage, Ra

P 0.2

0.0 1.0

0.8

0.6

0.4 ercentage, Vf

P 0.2

0.0 Af, CTRL Figure S9A.

Ascomycota;Aspergillus unclassified Basidiomycota;Malassezia_sympodialis Basidiomycota;Malassezia_globosa Basidiomycota;Malassezia_dermatis Basidiomycota;Malassezia_restricta Basidiomycota;Malassezia Basidiomycota;Malssezia_unclassified Ascomycota;Leptosphaerulina Basidiomycota;Rhodotorula Fi Fi Actinobacte Actinobacte Actinobacte Actinobacte Actinobacte Fi Actinobacte Actinobacte Fi Actinobacte Actinobacte Actinobacte Proteobacte Fi Fi Proteobacte Proteobacte Fi Proteobacte Fi Fi Fi Bacteroidetes; Bacteroidetes;Pr Actinobacte Fi Actinobacte Fi Fi Actinobacte Spearman correlation r r r r r r r r r r r r r micutes;Stap micutes;Streptococcus_the micutes;Anaerococcus micutes;Streptococcus_sanguinis micutes;Streptococcus_unclassifia micutes;Streptococcus micutes;Streptococcus_pneumoniae micutes; micutes;G micutes;Gemella micutes;Stap micutes;Stap micutes;Stap V r r r r r r r r r r r r r r r r r eillonella ia;Rothia ia; ia;Co ia;Co ia;Gordonia ia;Mycobacte ia;Actino ia; ia;Propionibacte ia;Propionibacte ia;unclassified ia;Micrococcus ia;Propionibacte r ia;Neisse ia; ia;Simonsiella ia;Neisse a P n K T P h h h h o ulicatella u ocu e a ylococcus_unclassifia ylococcus_capitis ylococcus ylococcus_epide r r r r v p r icella ynebacte ynebacte acoccus otella h r yromonas ia m r r ia_unclassifia ia yces r ium r r ium ium_unclassifia r r r ium_unclassifia ium ium_acnes r mophilus r midis b b le le b le b b le le Af, HIES

Basidiomycota;Malassezia_globosa Basidiomycota;Malassezia Ascomycota;Aspergillus Ascomycota;Candida Ascomycota;Penicillium Ascomycota;Debaryomyces Basidiomycota;Malassezia_restricta Basidiomycota;Rhodotorula Basidiomycota;Sporidiobolales_genus Basidiomycota;Malssezia_unclassified unclassified Ascomycota;Phaeococcomyces Basidiomycota;unclassified_Polyporales_genus Basidiomycota;Cryptococcus Basidiomycota;Pseudozyma Ascomycota;Dothioraceae_genus Actinobacte Fi Actinobacte Fi Fi Actinobacte Actinobacte Fi Actinobacte Fi Fi Fi Actinobacte Actinobacte Proteobacte Proteobacte Actinobacte Actinobacte Fi Fi Proteobacte Fi Proteobacte Actinobacte Proteobacte Spearman correlation Proteobacte Fi Fi Fi Bacteroidetes;Pr Fi Fi Fi Fi Fi Fi Actinobacte r r r r r r r r r r r r r r r r r r r micutes;Stap micutes; micutes;Stap micutes;Streptococcus_the micutes; micutes;Stap micutes;Gemella micutes;Stap micutes;Streptococcus_o micutes;Stap micutes;Lactobacillus micutes;Finegoldia micutes;Stap micutes;Stap micutes;Anaerococcus micutes;Streptococcus_pneumoniae micutes;G micutes;Streptococcus_unclassifia micutes;Streptococcus P V r r r r r r r r r r r r r r r r r eillonella eptoniphilus ia;Micrococcus ia;Co ia;Co ia;unclassified ia;Rothia ia; ia;A ia;Propionibacte ia;Propionibacte ia;Propionibacte ia;Actino r ia;Bu ia;Acid ia;Haemophilus ia;Ser ia;Neisse ia;N a n K h h h h h h h ulicatella ocu r e ylococcus_epide ylococcus ylococcus_unclassifia ylococcus_haemolyticus ylococcus_hominis ylococcus_aureus ylococcus_capitis o throbacter r r v r v ynebacte ynebacte r kholde otella osphingobium atia o r ia v m o r ia yces r ax r ia r r r ium ium_unclassifia alis r r r ium ium_acnes ium_unclassifia r mophilus r midis b le b le b b le le Figure S9B. N, CTRL N, HIES

Spearman correlation Spearman correlation

1

Bacteroidetes;Prevotella Firmicutes;Dolosigranulum Actinobacteria;Corynebacterium_unclassifiable Firmicutes;Staphylococcus_unclassifiable Actinobacteria;Corynebacterium Firmicutes;Streptococcus Proteobacteria;Neisseria_unclassifiable Proteobacteria;Neisseria Actinobacteria;unclassified Bacteroidetes;Prevotella Firmicutes;Finegoldia Firmicutes;Streptococcus_salivarius Firmicutes;Streptococcus_unclassifiable Proteobacteria;Simonsiella Firmicutes;Lactobacillus Firmicutes;Staphylococcus_aureus Firmicutes;Finegoldia Firmicutes;Staphylococcus_capitis Firmicutes;Dolosigranulum Firmicutes;Streptococcus_pneumoniae Actinobacteria;Corynebacterium_unclassifiable Firmicutes;Veillonella Actinobacteria;unclassified Actinobacteria;Corynebacterium Firmicutes;Anaerococcus Firmicutes;Staphylococcus_capitis Firmicutes;Staphylococcus Firmicutes;Streptococcus Firmicutes;Staphylococcus Firmicutes;Staphylococcus_unclassifiable Firmicutes;Staphylococcus_epidermidis Firmicutes;Staphylococcus_aureus Actinobacteria;Propionibacterium_unclassifiable Proteobacteria;Moraxella Firmicutes;Staphylococcus_epidermidis Firmicutes;Peptoniphilus Proteobacteria;Pseudomonas Actinobacteria;Propionibacterium_unclassifiable Proteobacteria;Haemophilus Firmicutes;Streptococcus_oralis Firmicutes;Anaerococcus Firmicutes;Staphylococcus_haemolyticus Actinobacteria;Propionibacterium_acnes Firmicutes;Lactococcus Actinobacteria;Propionibacterium_acnes Actinobacteria;Propionibacterium Actinobacteria;Propionibacterium a ia r us us us us r ula icta n n n n icta r r r yces ulina ipo r r m ametes r T enicillium eniopho P yptococcus P unclassified r ycota;Phoma aceae_ge r ycota;Candida m ycota;Ce ycota; m ycota; ycota;Aspergillus m m ycota;Aspergillus ycota;Malassezia ycota; ycota;Malassezia ycetaceae_ge idiobolales_ge ycota;Rhodoto ycota;Hyphodontia m r m m m m m m ycota;C Asco m m Asco m ycota;Saccharo ycota;Leptosphae Asco m Asco Asco Basidio Basidio m ycota;Malassezia_obtusa ycota;Malassezia_globosa Basidio ycota;Malassezia_rest Basidio ycota;Malassezia_globosa Basidio ycota;Malassezia_rest m Basidio Basidio m m m m ycota;Spo Asco Basidio ycota;Malssezia_unclassified ycota;Malssezia_unclassified Asco ycota;Malassezia_sympodialis ycota;Malassezia_sympodialis m m m m m ycota;Hymenochaetaceae_ge Basidio ycota;Saccharo m Basidio Basidio Basidio Basidio m Basidio Basidio Basidio Basidio Basidio ycota;unclassified_Dothio m Asco Basidio Asco Figure S9C. Ra, CTRL Ra, HIES

Spearman correlation Spearman correlation

Firmicutes;Streptococcus_pneumoniae Firmicutes;Streptococcus_unclassifiable Firmicutes;Streptococcus Firmicutes;Anaerococcus Bacteroidetes;Prevotella

Actinobacteria;Corynebacterium Firmicutes;Granulicatella Actinobacteria;Corynebacterium Actinobacteria;Corynebacterium_unclassifiable Actinobacteria;Corynebacterium_unclassifiable Firmicutes;Streptococcus Firmicutes;Staphylococcus_unclassifiable Firmicutes;Streptococcus_pneumoniae Firmicutes;Staphylococcus_capitis Firmicutes;Anaerococcus Firmicutes;Staphylococcus Firmicutes;Staphylococcus_aureus

Firmicutes;Staphylococcus_epidermidis Firmicutes;Staphylococcus_capitis Firmicutes;Finegoldia Actinobacteria;Propionibacterium_unclassifiable Firmicutes;Lactobacillus

Actinobacteria;unclassified Actinobacteria;Propionibacterium_unclassifiable Firmicutes;Staphylococcus Proteobacteria;Simonsiella Firmicutes;Staphylococcus_haemolyticus Firmicutes;Staphylococcus_unclassifiable Actinobacteria;Corynebacterium_kroppenstedtii Firmicutes;Staphylococcus_epidermidis Actinobacteria;Propionibacterium Actinobacteria;Propionibacterium_acnes Actinobacteria;Propionibacterium_acnes Actinobacteria;Propionibacterium us us ula icta icta n n r r r yptococcus unclassified r aceae_ge r ycota;Candida m ycota;Aspergillus ycota;Malassezia ycota;Malassezia idiobolales_ge ycota;Rhodoto r m m m ycota;C m Asco m Asco ycota;Malassezia_globosa ycota;Malassezia_globosa Basidio Basidio ycota;Malassezia_rest ycota;Malassezia_rest ycota;Dothio Basidio m m m m m ycota;Spo Basidio ycota;Malssezia_unclassified ycota;Malssezia_unclassified ycota;Malassezia_sympodialis m m m m Asco Basidio Basidio Basidio Basidio Basidio Basidio Basidio Basidio Figure S9D.

Vf, CTRL Spearman correlation Vf, HIES Spearman correlation

Actinobacteria;Propionibacterium_acnes Firmicutes;Peptoniphilus Actinobacteria;Propionibacterium Actinobacteria;Actinomyces Actinobacteria;Micrococcus Bacteroidetes;Prevotella Firmicutes;Streptococcus_sanguinis Proteobacteria;Paracoccus Firmicutes;Veillonella Actinobacteria;Actinomyces Firmicutes;Staphylococcus_aureus Proteobacteria;Simonsiella Firmicutes;Staphylococcus_capitis Firmicutes;Streptococcus_sanguinis Firmicutes;Finegoldia Firmicutes;Streptococcus_unclassifiable Firmicutes;Staphylococcus Firmicutes;Streptococcus_thermophilus Firmicutes;Streptococcus_pneumoniae Actinobacteria;Corynebacterium Firmicutes;Staphylococcus_unclassifiable Actinobacteria;Corynebacterium_unclassifiable Actinobacteria;Propionibacterium_unclassifiable Actinobacteria;Rothia Firmicutes;Anaerococcus Actinobacteria;Corynebacterium_unclassifiable Firmicutes;Veillonella Proteobacteria;Neisseria_unclassifiable Proteobacteria;Neisseria_meningitidis Proteobacteria;Neisseria Firmicutes;Gemella Firmicutes;Alloiococcus Bacteroidetes;Prevotella Firmicutes;Granulicatella Bacteroidetes;Porphyromonas Firmicutes;Streptococcus_salivarius Fusobacteria;Fusobacterium Firmicutes;Lactobacillus Proteobacteria;Neisseria Firmicutes;Streptococcus Proteobacteria;Neisseria_unclassifiable Firmicutes;Streptococcus_unclassifiable Firmicutes;Gemella Firmicutes;Streptococcus Actinobacteria;Corynebacterium_kroppenstedtii Firmicutes;Staphylococcus_capitis Firmicutes;Bacillus Firmicutes;Streptococcus_pneumoniae Actinobacteria;Rothia Firmicutes;Granulicatella Firmicutes;Staphylococcus_epidermidis Actinobacteria;Gordonia Proteobacteria;Serratia Firmicutes;Staphylococcus_epidermidis Proteobacteria;Acinetobacter Actinobacteria;Kocuria Proteobacteria;Pseudomonas Firmicutes;Staphylococcus_haemolyticus Actinobacteria;Corynebacterium Firmicutes;Staphylococcus Firmicutes;Staphylococcus_hominis Firmicutes;Staphylococcus_haemolyticus Firmicutes;Staphylococcus_unclassifiable Firmicutes;Streptococcus_thermophilus Actinobacteria;unclassified.1 Firmicutes;Streptococcus_oralis Actinobacteria;Propionibacterium_unclassifiable Firmicutes;Lactococcus Actinobacteria;unclassified Actinobacteria;Propionibacterium_acnes Firmicutes;Anaerococcus Actinobacteria;Propionibacterium us us us us ula ula icta icta n n n n r r r r matis r ametes r T yptococcus unclassified r ycota;Phoma aceae_ge ureobasidium r ycota;Candida A m ycota; m tae_sedis;Mucor ycota;Sistotrema ycota;Aspergillus ycota;Aspergillus m ycota;Malassezia ycota;Malassezia r ycetaceae_ge idiobolales_ge ycota;Rhodoto ycota;Rhodoto m r m m m m m ycota;C Asco m m ycota; Asco m m Asco Asco Basidio Basidio ycota;Malassezia_globosa ycota;Malassezia_globosa Basidio Basidio ycota;Malassezia_rest ycota;Malassezia_rest ycota;Dothio ycota;Malassezia_de ylum_ince Basidio Basidio Asco m m m m m h ycota;Spo Basidio ycota;Malssezia_unclassified ycota;Malssezia_unclassified m ycota;Malassezia_sympodialis ycota;Malassezia_sympodialis m m m m m Asco ycota;Mycosphaerellaceae_ge ycota;Saccharo Basidio Basidio Basidio Basidio m Basidio Fungi_p m Basidio Basidio Basidio Basidio Basidio Asco Asco