Supplementary file 1.
(A) Troy sample details (B) SEM-EDS results from nodule. For each replicate, upper value is weight %, lower value is atomic %. (C) Common chemical constituents of renal and bladder calculi (kidney and bladder stones) and Troy nodules. + - presence, ND- not detected, Unk- unknown, RF- Relative Frequency in modern populations (C.Y.C Pak (ed.) Pak , Martinus Nijhoff Publishing, Boston). (D) Relative frequency of admixed calculi (kidney and bladder stones) in modern (grey shading) populations and archaeological findings (modified from Pak, 1987). Acronyms correspond to Table C. References cited herein. *1 Main constituent of bladder stone listed as ammonium acid urate and oxalate. *2 Majority of calculus determined to be calcium carbonate (calcite). Where not specifically given, relative proportions of all mineral components were estimated. *3 Minor constituents of calcium carbonate. *4 No other (minor) elements were provided thus composition was assumed to be 100%. ND – not determined/detected. (E) Mitochondrial results summary; unique reads mapped to the revised Cambridge Reference Sequence with minimum length of 35 bp and minimum mapping quality of 30. (F) Sex identification of all libraries after Skoglund et al. (2013). Libraries were mapped to a hard masked version of hg38 and restricted to reads of minimum length 35 bp and minimum mapping quality of 30. (G) Summary of unique shotgun reads (from nodules, ulna, sediment and associated blanks) of minimum length 35 bp and minimum mapping quality of 30, mapping to chromosome X, Y, autosomes and mitochondrion of the hard masked hg38. Nodule pooled =Nod2-UDG + Nod1. (H) Staphylococcus saprophyticus modern strains. (I) Gardnerella vaginalis modern strains. * F = full, S = scaffold; ** BWH = Brigham and Women’s Hospital, HMP = Human Microbiome Project, MWH = Magee-Womens Hospital, VCU = VCU Women’s Health Clinic (J) Troy DNA extraction details. *Demin. = demineralization; digest = digestion buffer (K) HTS data sets. (L) Summary of unique shotgun reads (from nodules, ulna, sediment and associated blanks) of minimum length 35 bp and minimum mapping quality of 30, mapping to Staphylococcus saprophyticus and Gardnerella vaginalis. Nodule pooled =Nod2-UDG + Nod1_1h-nonU + Nod2-nonU + Nod1_1h-UDG). (M) Kinetic analysis of ancient PC1 β-lactamase (N) S. saprophyticus Clade P specific genes. Locus tags refer to annotation of ATCC 15305 available at NCBI. (O) Non-synonymous variants shared between S. saprophyticus Clade P and isolate 55. REF is reference allele in ATCC15305, Clade P and isolate 55. ALT is allele in the remaining Clade E isolates. Locus tags refer to annotation of ATCC 15305 available at NCBI.