Supplementary appendix

Table S1. All 303 microbial taxa with minimum relative abundance of 0.1% in pre, pos or neg. SEE ATTACHED FILE.

Table S2. Distributions of characteristics and urinary measurements in postmenopausal cases of breast cancer and matched control women.

CharacteristicsAge (years) Contro

lCase

1st Quantile 59.00 57.50

Median 61.00 63.00

3rd Quantile 64.25 67.00

Body mass index (BMI, Kg/M2) Control

Case

1st Quantile 23.10 24.15

Median 26.78 27.92

3rd Quantile 31.05 32.96

Urine prostaglandin E metabolites (PGE-M)PGE-M1 (nanogram/mg creatinine) Contro

lCase

1st Quantile 10.50 11.35

Median 12.60 13.55

3rd Quantile 16.85 17.24

PGE-M2 (nanogram/mg creatinine) Control

Case

1st Quantile 1.82 1.80Median 2.37 3.003rd Quantile 4.03 4.18

Estrogens and estrogen metabolites (EM)Total estrogens + EM (picomole/mg creatinine) Contro

lCase

1st Quantile 12.09 14.16

Median 18.34 21.22

3rd Quantile 25.43 32.93

Parents (estrone + estradiol, picomole/mg creatinine) Control

Case

1st Quantile 4.11 4.24Median 5.76 6.71

Table S3. Associations of urinary estrogens and prostaglandin E levels with the IgA-stained and -unstained fecal microbiome alpha diversity among postmenopausal women with breast cancer and matched control women.*

Total urinary estrogens and estrogen metabolitesControls Cases All participants

Alpha diversity metric IgA-positive

IgA-negative

IgA-positive

IgA-negative

IgA-positive

IgA-negative

Observed species 0.241 0.013 0.563 0.219 0.385 0.018Chao1 index 0.215 0.014 0.558 0.214 0.393 0.017PD_whole_tree 0.398 0.012 0.107 0.132 0.140 0.014Shannon index 0.083 0.024 0.770 0.120 0.272 0.018

Urinary prostaglandin E metabolite (PGE-M), Lab 1Controls Cases All participants

Alpha diversity metric IgA-positive

IgA-negative

IgA-positive

IgA-negative

IgA-positive

IgA-negative

Observed species 0.584 0.571 0.542 0.504 0.877 0.788Chao1 index 0.560 0.594 0.541 0.495 0.862 0.810PD_whole_tree 0.545 0.643 0.682 0.822 0.992 0.993Shannon index 0.529 0.708 0.978 0.930 0.831 0.996

Urinary prostaglandin E metabolite (PGE-M), Lab 2Controls Cases All participants

Alpha diversity metric IgA-positive

IgA-negative

IgA-positive

IgA-negative

IgA-positive

IgA-negative

Observed species 0.314 0.529 0.617 0.504 0.225 0.258Chao1 index 0.304 0.516 0.593 0.482 0.215 0.251PD_whole_tree 0.297 0.467 0.462 0.532 0.204 0.278Shannon index 0.662 0.477 0.698 0.915 0.423 0.461

* P-values from Spearman correlation tests are presented.

Figure S1. First three principal components (PC1, PC2, PC3) of Bray Curtis dissimilarity, unweighted UniFrac distance, and weighted UniFrac distance for all specimens. Distinct and tightly clustered distributions are evident for the three types of quality control (QC) specimens: green, water; light blue, Chemostat A; and dark blue, Chemostat B. The 96 case-control specimens are yellow (unsorted), red (IgA-negative), and orange (IgA-positive).

Figure S2. Box plots of first principal components (PC1) of unweighted UniFrac distances. (From left) IgA-positive taxa in controls (first box) and in breast cancer cases (second box, P=0.04). IgA-negative taxa in controls (third box) and in cases (fourth box, P=0.03). All IgA-positive taxa (fifth box) and all IgA-negative taxa (sixth box). All taxa in controls (seventh box) and in cases (eighth box, P=0.07). Results are also presented in Table 1, including the next two principal components (PC2 and PC3).

Figure S3. Metabolism pathways in fecal specimens from all 96 participants. (Left) In each participant (columns), relative abundance of each pathway in the unsorted (top), IgA-positive (middle), and IgA-negative (bottom) microbiota.(Right) Color coding for KEGG assignments of the Level 2 pathways.

IgA-negative

IgA-positive

Unsorted

Figure S4. Beta diversity comparisons [distributions of observed (Y-axes) and expected (X-axes) -log P-values] of metabolic pathways in the unsorted (Pre), IgA-stained (pos), and IgA-unstained (neg) fecal microbiota of postmenopausal breast cancer cases versus matched controls. (Top row) Level 1 (L1) pathways based on PICRUSt and KEGG.(Middle row) Level 2 (L2) pathways based on PICRUSt and KEGG.(Bottom row) Level 3 (L3) pathways based on PICRUSt and KEGG.