Supplementary Figure 1. Scatterplots showing the assignment of Total RNA-seq reads and measures of human genes and bacterial species detected in each sample. (A) Bacterial versus human-derived reads (millions). (B) Number of genes detected (minimum 20 assigned reads) versus human-derived reads (millions). (C) Number of bacterial species (minimum 20 assigned reads) versus bacterial-derived reads (millions). (D) Shannon diversity versus the number of bacterial-derived reads (millions). Supplementary Table 1. Patient #1 CT alignment CT gene CT protein SLIMM_all SLIMM_unique ompA Major Outer Membrane Protein 211 211 tmRNA noncoding RNA 173 173 omcA 9kDa-Cysteine-Rich Lipoprotein 100 100 omcB 60kDa Cysteine-Rich OMP 66 66 CT_398.1 noncoding RNA 61 61 groEL_1 HSP-60 39 39 ndk Nucleoside-2-P Kinase 33 33 CT_858 predicted Protease containing IRBP and DHR domains 29 29 tufA Elongation Factor Tu 28 28 hctB Histone-like Protein 2 24 24 yscC probable Yop proteins translocation protein C/general secretion pathway protein 23 23 CT_081 CHLTR T2 Protein 26 20 rpoC RNA Polymerase Beta' 24 20 CT_671 hypothetical protein 20 20 clpC ClpC Protease ATPase 19 19 CT_578 hypothetical protein 19 18 CT_664 adenylate cyclase-like protein 18 17 rho Transcription Termination Factor 15 15 glgA Glycogen Synthase 15 15 CT_456 hypothetical protein 14 14 CT_875 hypothetical protein 14 14 CT_708 SWF/SNF family helicase 13 13 dhnA Predicted 1%2C6-Fructose biphosphate aldolase (dehydrin family) 12 12 clpX CLP Protease ATPase 15 12 CT_082 hypothetical protein 13 11 nusA Transcription antitermination factor 11 11 CT_266 hypothetical protein 11 11 ihfA Integration Host Factor Alpha 11 11 tal Transaldolase 11 11 fusA Elongation Factor G 11 11 CT_579 hypothetical protein 12 11 recA hypothetical protein 10 10 CT_043 hypothetical protein 9 9 rl1 L1 Ribosomal Protein 11 9 yprS hypothetical protein 9 9 pmpC Putative outer membrane protein C 9 9 secY Translocase 9 9 lcrH_1 LoW Calcium Response Protein H 10 9 ung Uracil DNA Glycosylase 9 9 CT_610 hypothetical protein 10 9 pyrH UMP Kinase 10 9 ftsW Cell Division Protein FtsW 9 9 nrdA Ribonucleoside Reductase%2C Large Chain 9 9 pmpE Putative Outer Membrane Protein E 12 9 pmpH Putative Outer Membrane Protein H 9 9 CT_001 hypothetical protein 8 8 gyrA_1 DNA Gyrase Subunit A 8 8 pmpB Putative outer membrane protein B 8 8 rs5 S5 Ribosomal Protein 8 8 dnaE DNA Pol III Alpha 8 8 CT_546 predicted OMP 8 8 porB Outer Membrane Protein Analog 8 8 tktB Transketolase 8 8 pmpD Putative Outer Membrane Protein D 8 8 glgB 1%2C 4-alpha-glucan branching enzyme 8 8 pmpF Putative Outer Membrane Protein F 11 8 lcrD LoW Calcium Response D 10 7 trxB Thioredoxin Reductase 7 7 CT_214 hypothetical protein 8 7 CT_289 hypothetical protein 7 7 gidA FAD-dependent oxidoreductase 7 7 gapA Glyceraldehyde-3-P Dehydrogenase 7 7 rl3 L3 Ribosomal Protein 11 7 CT_556 hypothetical protein 7 7 CT_622 CHLPN 76kDa Homolog 7 7 yceA hypothetical protein 7 7 CT_663 hypothetical protein 7 7 fabF Acyl Carrier Protein Synthase 9 7 htrA DO Serine Protease 7 7 pheS Phenylalanyl tRNA Synthetase%2C Alpha 7 7 pmpI Putative Outer Membrane Protein I 7 7 dcd Deoxycytidine triphosphate deaminase family protein 6 6 ytgC Integral Membrane Protein 6 6 CT_115 hypothetical protein 6 6 CT_136 predicted Lysophospholipase esterase 6 6 yaeT Omp85 Analog 6 6 CT_283 hypothetical protein 6 6 rpoB RNA Polymerase Beta 10 6 CT_503 hypothetical protein 6 6 rl6 L6 Ribosomal Protein 6 6 rl2 L2 Ribosomal Protein 6 6 uhpC Hexosphosphate Transport 6 6 lpdA Lipoamide Dehydrogenase 6 6 CT_560 hypothetical protein 7 6 CT_565 hypothetical protein 6 6 CT_621 hypothetical protein 6 6 CT_623 CHLPN 76kDa Homolog 6 6 CT_665 hypothetical protein 10 6 CT_668 hypothetical protein 7 6 pgk Phosphoglycerate Kinase 6 6 CT_814 hypothetical protein 7 6 ftsY Cell Division Protein FtsY 6 6 nrdB Ribonucleoside Reductase%2C Small Chain 6 6 pmpG Putative Outer Membrane Protein G 6 6 gatB Glu-tRNA Gln Amidotransferase B Subunit 7 5 ssb SS DNA Binding Protein 5 5 CT_065 ADP/ATP Translocase 5 5 clpB Clp Protease ATPase 6 5 CT_365 hypothetical protein 5 5 mdhC Malate Dehydrogenase 5 5 gltX Glutamyl-tRNA Synthetase 6 5 CT_700 hypothetical protein 5 5 rs18 S18 Ribosomal Protein 5 5 rl35 L35 Ribosomal Protein 5 5 CT_837 hypothetical protein 6 5 ftsH ATP-dependent zinc protease 5 5 lepA GTPase 4 4 ytgA Solute Protein Binding Family 4 4 ltuB hypothetical protein 8 4 CT_181 hypothetical protein 4 4 accD AcCoA Carboxylase/Transferase Beta 4 4 sodM Superoxide Dismutase (Mn) 4 4 lon Lon ATP-dependent protease 4 4 def Polypeptide Deformylase 4 4 CT_388 hypothetical protein 4 4 yrbH GutQ/KpsF Family Sugar-P Isomerase 4 4 rs7 S7 Ribosomal Protein 4 4 tsp Tail-Specific Protease 4 4 recJ ssDNA Exonuclease 4 4 cdsA Phosphatidate Cytidylytransferase 4 4 oppA_4 oligopeptide Binding Lipoprotein 4 4 fliY Glutamine Binding Protein 4 4 CT_504 hypothetical protein 4 4 lpxC UDP-3-O-Acyl GlcNAc Deacetylase 4 4 gspD Gen. Secretion Protein D 4 4 folP Dihydropteroate Synthase 4 4 pkn5 S/T Protein Kinase 4 4 tsf Elongation Factor TS 8 4 CT_685 ABC Transporter ATPase 4 4 CT_694 hypothetical protein 4 4 mreB Rod Shape Protein-Sugar Kinase 4 4 pgm Phosphoglycerate Mutase 4 4 mfd Transcription-Repair Coupling 4 4 murD UDP-N-acetylmuramoylalanine-D-glutamate ligase 7 4 ldh Leucine Dehydrogenase 4 4 aas Acylglycerophosphoethanolamine Acyltransferase 4 4 CT_790 hypothetical protein 4 4 yccA Transport Permease 4 4 xerD Integrase/recombinase 4 4 CT_016 hypothetical protein 3 3 sucB_1 Dihydrolipoamide Succinyltransferase 3 3 lcrE LoW Calcium Response E 3 3 groES 10KDa Chaperonin 3 3 zwf Glucose-6-P Dehyrogenase 3 3 gyrB_1 DNA Gyrase Subunit B 4 3 gseA KDO Transferase 3 3 murE UDP-N-acetylmuramoylalanylglutamyl DAP Ligase 3 3 mrsA_1 Phosphomannomutase 3 3 rl7 L7/L12 Ribosomal Protein 3 3 rl11 L11 Ribosomal Protein 5 3 lysC Aspartokinase III 4 3 CT_372 hypothetical protein 3 3 pgi Glucose-6-P Isomerase 3 3 dnaK HSP-70 3 3 lpxK probable tetraacyldisaccharide 4' kinase 3 3 CT_444.1 hypothetical protein 4 3 CT_460 SWIB (YM74) complex protein 3 3 yaeI phosphohydrolase 3 3 rl4 L4 Ribosomal Protein 7 3 yciA Acyl-CoA Thioester Hydrolase 3 3 mip FKBP-type peptidyl-prolyl cis-trans isomerase 3 3 yscL Yop proteins translocation protein L 3 3 CT_567 hypothetical protein 4 3 CT_577 hypothetical protein 4 3 tolB component of a macromolecule transport system 3 3 ahpC Thio-specific Antioxidant (TSA) Peroxidase 3 3 CT_611 hypothetical protein 4 3 CT_667 hypothetical protein 5 3 fliN Flagellar Motor Switch Domain/YscQ family 3 3 yfhO_1 NifS-related enzyme 3 3 secA_2 Protein Translocase 3 3 pcnB_2 Poly A Polymerase 6 3 ribD Riboflavin Deaminase 3 3 CT_734 hypothetical protein 3 3 ftsK Cell Division Protein FtsK 3 3 hctA Histone-Like Developmental Protein 3 3 CT_768 hypothetical protein 3 3 CT_775 snGlycerol 3-P Acyltransferase 3 3 tyrP_2 Tyrosine Transport 3 3 CT_824 Zinc Metalloprotease (insulinase family) 3 3 htrB Acyltransferase 2 2 CT_017 hypothetical protein 2 2 CT_018 hypothetical protein 2 2 ileS Isoleucyl-tRNA Synthetase 2 2 rnhB_2 Ribonuclease HII 2 2 CT_036 hypothetical protein 2 2 pepA Leucyl Aminopeptidase A 2 2 CT_049 hypothetical protein 2 2 gcpE hypothetical protein 2 2 ytgB_1 rRNA methylase 2 2 CT_084 Phopholipase D Superfamily 6 2 malQ 4-alpha glucanotransferase 2 2 yscU Yop proteins translocation protein U 5 2 efp_1 Elongation Factor P 2 2 rs9 S9 Ribosomal Protein 2 2 CT_138 Dipeptidase 4 2 CT_147 hypothetical protein 2 2 surE SurE-like Acid Phosphatase 2 2 yqfU hypothetical protein 7 2 CT_223 hypothetical protein 2 2 incB Inclusion Membrane Protein B 2 2 fabH Oxoacyl Carrier Protein Synthase III 2 2 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 2 2 pdhA Pyruvate Dehydrogenase Alpha 2 2 yhfO NifS family of pyridoxal phosphate-dependent enzymes 2 2 nqr2 NADH (Ubiquinone) Dehydrogenase 2 2 nqr3 NADH (Ubiquinone) Oxidoreductase%2C Gamma 2 2 CT_309 hypothetical protein 2 2 CT_326.2 hypothetical protein 2 2 xseA Exodoxyribonuclease VII 2 2 pdhA/B (pyruvate) Oxoisovalerate Dehydrogenase Alpha/Beta Fusion 2 2 yyaL multidomain protein family 2 2 CT_358 hypothetical protein 3 2 artJ Arginine Binding Protein 2 2 CT_384 hypothetical protein 4 2 CT_387 hypothetical protein 2 2 proS Prolyl tRNA Synthetase 2 2 sucB_2 Dihydrolipoamide Succinyltransferase 2 2 dksA DnaK Suppressor 5 2 clpP_1 CLP Protease 3 2 rs10 S10 Ribosomal Protein 2 2 rs12 S12 Ribosomal Protein 2 2 yebC YebC family 2 2 pheT phenylalanyl tRNA Synthetase Beta 2 2 CT_482 hypothetical protein 2 2 CT_484 hypothetical protein 2 2 pgsA_1 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 2 2 rl17 L17 Ribosomal Protein 2 2 rs13 S13 Ribosomal Protein 2 2 rl5 L5 Ribosomal Protein 3 2 rl24 L24 Ribosomal Protein 7 2 rl16 L16 Ribosomal Protein 2 2 CT_529 hypothetical protein 2 2 aspS Aspartyl tRNA Synthetase 2 2 hisS Histidyl tRNA Synthetase 2 2 fmu RNA Methyltransferase 2 2 yscJ Yop proteins translocation lipoprotein J 3 2 yscT Yop proteins translocation protein T 2 2 thrS Threonyl tRNA Synthetase 2 2 minD chromosome partitioning ATPase-CHLTR plasmid protein homolog GP5D 2 2 uvrB Exinuclease ABC Subunit B 2 2 pal Peptidoglycan-Associated Lipoprotein 2 2 uvrD DNA Helicase 2 2 CT_619 hypothetical protein 2 2 CT_620 hypothetical protein 2 2 CT_635 hypothetical protein 2 2 greA Transcription Elongation Factor G 2 2 recB Exodeoxyribonuclease V%2C Beta 2 2 CT_642 hypothetical protein 4 2 CT_652.1 hypothetical protein 2 2 CT_659 hypothetical protein 2 2 gyrB_2 DNA Gyrase Subunit B 2 2 CT_666