#Additional data file 1 # Table S1. Distribution of network microbes by phylum. Phylum N Actinobacteria 48 Apicomplexa 1 Bacteroidetes 17 Chlorobi 8 Chloroflexi 5 Crenarchaeota 2 Cyanobacteria 17 Euryarchaeota 12 Firmicutes 196 Fusobacteria 3 Proteobacteria 448 Spirochaetes 13 Thermi 4 Total 774 Table S2: Distribution of network microbes by habitat. Habitat N Aquatic 64 Aquatic Host 17 Aquatic Host Soil 48 Aquatic Marine 10 Aquatic Marine Soil 2 Aquatic Soil 29 Host 327 Host Marine 1 Host Soil 31 Marine 101 none 52 Soil 92 Total 774 Table S3a. Frequency of intra-habitat and inter-habitat connections at the 80% identity cutoff. A and B: habitats. Obs: observed number of connections. Exp: expected number of connections based on random selection. Prob: probability of this connection by chance. Ratio: Obs:Exp. Habitat 80% A B obs exp prob ratio Aquatic Aquatic 73 35.2730939 0.006837196 2.069566118 Aquatic Aquatic Host 14 18.73883113 0.00363226 0.747111701 Aquatic Aquatic Host Soil 37 52.90964085 0.010255794 0.699305446 Aquatic Aquatic Marine 25 11.02284184 0.002136624 2.268017663 Aquatic Aquatic Marine Soil 3 2.204568369 4.27E-04 1.360810598 Aquatic Aquatic Soil 16 31.96624135 0.006196209 0.500528036 Aquatic Host 97 360.4469283 0.069867596 0.269110353 Aquatic Host Marine 0 1.102284184 2.14E-04 0 Aquatic Host Soil 31 34.17080971 0.006623534 0.907207065 Aquatic Marine 152 111.3307026 0.0215799 1.365301722 Aquatic none 33 57.31877758 0.011110443 0.575727561 Aquatic Soil 27 101.410145 0.019656938 0.266245552 Aquatic Host Aquatic Host 21 2.48875101 4.82E-04 8.437967445 Aquatic Host Aquatic Host Soil 7 14.05412335 0.002724195 0.498074467 Aquatic Host Aquatic Marine 7 2.927942365 5.68E-04 2.390757443 Aquatic Host Aquatic Marine Soil 1 0.585588473 1.14E-04 1.707683888 Aquatic Host Aquatic Soil 3 8.491032857 0.001645868 0.353313908 Aquatic Host Host 34 95.74371532 0.01855858 0.355114692 Aquatic Host Host Marine 0 0.292794236 5.68E-05 0 Aquatic Host Host Soil 3 9.07662133 0.001759376 0.330519462 Aquatic Host Marine 21 29.57221788 0.005732161 0.710125973 Aquatic Host none 2 15.2253003 0.002951212 0.131360299 Aquatic Host Soil 3 26.93706975 0.005221374 0.111370688 Aquatic Host Soil Aquatic Host Soil 78 19.84111532 0.003845923 3.931230616 Aquatic Host Soil Aquatic Marine 6 8.267131382 0.001602468 0.725765652 Aquatic Host Soil Aquatic Marine Soil 0 1.653426276 3.20E-04 0 Aquatic Host Soil Aquatic Soil 14 23.97468101 0.004647157 0.583949375 Aquatic Host Soil Host 707 270.3351962 0.052400697 2.615271744 Aquatic Host Soil Host Marine 0 0.826713138 1.60E-04 0 Aquatic Host Soil Host Soil 44 25.62810729 0.00496765 1.716864984 Aquatic Host Soil Marine 42 83.49802696 0.016184925 0.503005898 Aquatic Host Soil none 39 42.98908319 0.008332833 0.907207065 Aquatic Host Soil Soil 56 76.05760872 0.014742704 0.736283995 Aquatic Marine Aquatic Marine 1 0.861159519 1.67E-04 1.161225044 Aquatic Marine Aquatic Marine Soil 1 0.344463808 6.68E-05 2.903062609 Aquatic Marine Aquatic Soil 3 4.99472521 9.68E-04 0.600633643 Aquatic Marine Host 25 56.31983254 0.010916812 0.443893365 Aquatic Marine Host Marine 0 0.172231904 3.34E-05 0 Aquatic Marine Host Soil 5 5.339189018 0.001034927 0.936471809 Aquatic Marine Marine 30 17.39542228 0.003371859 1.724591649 Aquatic Marine none 7 8.956058998 0.001736007 0.781593779 Aquatic Marine Soil 4 15.84533515 0.003071397 0.252440227 Aquatic Marine Soil Aquatic Marine Soil 0 0.034446381 6.68E-06 0 Aquatic Marine Soil Aquatic Soil 2 0.998945042 1.94E-04 2.002112144 Aquatic Marine Soil Host 8 11.26396651 0.002183362 0.710229384 Aquatic Marine Soil Host Marine 0 0.034446381 6.68E-06 0 Aquatic Marine Soil Host Soil 2 1.067837804 2.07E-04 1.872943619 Aquatic Marine Soil Marine 7 3.479084457 6.74E-04 2.01202359 Aquatic Marine Soil none 3 1.7912118 3.47E-04 1.674843813 Aquatic Marine Soil Soil 4 3.16906703 6.14E-04 1.262201134 Aquatic Soil Aquatic Soil 9 7.242351555 0.001403829 1.242690296 Aquatic Soil Host 92 163.3275144 0.031658754 0.563285374 Aquatic Soil Host Marine 0 0.499472521 9.68E-05 0 Aquatic Soil Host Soil 16 15.48364815 0.003001289 1.033348203 Aquatic Soil Marine 46 50.44672462 0.009778392 0.911853056 Aquatic Soil none 32 25.97257109 0.00503442 1.232069012 Aquatic Soil Soil 50 45.95147193 0.00890705 1.088104426 Host Host 1552 920.8292621 0.178489874 1.685437316 Host Host Marine 0 5.631983254 0.001091681 0 Host Host Soil 112 174.5914809 0.033842117 0.641497509 Host Marine 159 568.8303087 0.1102598 0.279520971 Host none 252 292.8631292 0.056767422 0.860470216 Host Soil 414 518.1424594 0.100434669 0.799008058 Host Marine Host Marine 0 0.008611595 1.67E-06 0 Host Marine Host Soil 0 0.533918902 1.03E-04 0 Host Marine Marine 3 1.739542228 3.37E-04 1.724591649 Host Marine none 0 0.8956059 1.74E-04 0 Host Marine Soil 0 1.584533515 3.07E-04 0 Host Soil Host Soil 19 8.275742978 0.001604137 2.295866371 Host Soil Marine 36 53.92580908 0.010452764 0.667583864 Host Soil none 38 27.76378289 0.005381621 1.368689568 Host Soil Soil 86 49.12053896 0.00952133 1.750795122 Marine Marine 198 87.84688253 0.01702789 2.253921759 Marine none 46 90.45619587 0.017533669 0.508533435 Marine Soil 48 160.037885 0.031021106 0.299928982 none none 18 23.28575339 0.004513618 0.773004837 Soil none 74 82.39574278 0.015971262 0.898104653 Soil Soil 161 72.88854169 0.014128424 2.208851985 Table S3b. Identical to Table S3a, but at a 90% cutoff level. This table serves as a control to verify that the signal is also present when cutoff levels are increased. Phylum 90% A B obs exp prob ratio Aquatic Aquatic 34 14.21809997 0.005936576 2.391318113 Aquatic Aquatic Host 12 9.075382962 0.003789304 1.322258251 Aquatic Aquatic Host Soil 7 26.01609782 0.010862671 0.269064179 Aquatic Aquatic Marine 11 4.235178715 0.001768342 2.597292993 Aquatic Aquatic Marine Soil 1 1.210051062 5.05E-04 0.826411407 Aquatic Aquatic Soil 3 10.89045955 0.004547165 0.275470469 Aquatic Host 8 170.6171997 0.071238914 0.04688859 Aquatic Host Marine 0 0.605025531 2.53E-04 0 Aquatic Host Soil 11 15.12563827 0.006315507 0.727242038 Aquatic Marine 41 42.35178715 0.017683418 0.968081934 Aquatic none 5 24.20102123 0.010104811 0.206602852 Aquatic Soil 9 36.30153185 0.015157216 0.247923422 Aquatic Host Aquatic Host 20 1.448199409 6.05E-04 13.81025284 Aquatic Host Aquatic Host Soil 2 8.303009944 0.00346681 0.240876503 Aquatic Host Aquatic Marine 4 1.351652782 5.64E-04 2.959339895 Aquatic Host Aquatic Marine Soil 0 0.386186509 1.61E-04 0 Aquatic Host Aquatic Soil 0 3.475678581 0.001451223 0 Aquatic Host Host 9 54.45229777 0.022735824 0.165282281 Aquatic Host Host Marine 0 0.193093255 8.06E-05 0 Aquatic Host Host Soil 0 4.827331363 0.002015587 0 Aquatic Host Marine 6 13.51652782 0.005643644 0.443900984 Aquatic Host none 0 7.72373018 0.00322494 0 Aquatic Host Soil 0 11.58559527 0.004837409 0 Aquatic Host Soil Aquatic Host Soil 67 11.90098092 0.004969094 5.629788036 Aquatic Host Soil Aquatic Marine 2 3.874737974 0.001617845 0.516163935 Aquatic Host Soil Aquatic Marine Soil 0 1.107067992 4.62E-04 0 Aquatic Host Soil Aquatic Soil 7 9.963611932 0.004160172 0.702556467 Aquatic Host Soil Host 402 156.0965869 0.065176028 2.57532857 Aquatic Host Soil Host Marine 0 0.553533996 2.31E-04 0 Aquatic Host Soil Host Soil 18 13.83834991 0.005778017 1.300733116 Aquatic Host Soil Marine 7 38.74737974 0.016178447 0.180657377 Aquatic Host Soil none 16 22.14135985 0.009244827 0.722629509 Aquatic Host Soil Soil 22 33.21203977 0.01386724 0.662410383 Aquatic Marine Aquatic Marine 0 0.315385649 1.32E-04 0 Aquatic Marine Aquatic Marine Soil 0 0.180220371 7.52E-05 0 Aquatic Marine Aquatic Soil 0 1.621983338 6.77E-04 0 Aquatic Marine Host 10 25.41107229 0.010610051 0.393529241 Aquatic Marine Host Marine 0 0.090110185 3.76E-05 0 Aquatic Marine Host Soil 2 2.252754636 9.41E-04 0.887801968 Aquatic Marine Marine 11 6.30771298 0.002633701 1.743896724 Aquatic Marine none 0 3.604407417 0.001504972 0 Aquatic Marine Soil 1 5.406611126 0.002257458 0.184958743 Aquatic Marine Soil Aquatic Marine Soil 0 0.025745767 1.07E-05 0 Aquatic Marine Soil Aquatic Soil 1 0.463423811 1.93E-04 2.157852006 Aquatic Marine Soil Host 0 7.260306369 0.003031443 0 Aquatic Marine Soil Host Marine 0 0.025745767 1.07E-05 0 Aquatic Marine Soil Host Soil 1 0.643644182 2.69E-04 1.553653445 Aquatic Marine Soil Marine 0 1.802203709 7.52E-04 0 Aquatic Marine Soil none 0 1.029830691 4.30E-04 0 Aquatic Marine Soil Soil 0 1.544746036 6.45E-04 0 Aquatic Soil Aquatic Soil 5 2.085407149 8.71E-04 2.397613341 Aquatic Soil Host 26 65.34275732 0.027282988 0.397901788 Aquatic Soil Host Marine 0 0.231711905 9.67E-05 0 Aquatic Soil Host Soil 5 5.792797635 0.002418705 0.863140803 Aquatic Soil Marine 14 16.21983338 0.006772373 0.863140803 Aquatic Soil none 13 9.268476216 0.003869927 1.402603804 Aquatic Soil Soil 17 13.90271432 0.005804891 1.222782804 Host Host 953 511.851599 0.213716743 1.861867779 Host Host Marine 0 3.630153185 0.001515722 0 Host Host Soil 41 90.75382962 0.03789304 0.451771569 Host Marine 38 254.1107229 0.106100511 0.149541112 Host none 74 145.2061274 0.060628863 0.509620367 Host Soil 171 217.8091911 0.090943295 0.785090836 Host Marine Host Marine 0 0.006436442 2.69E-06 0 Host Marine Host Soil 0 0.321822091 1.34E-04 0 Host Marine Marine 1 0.901101854 3.76E-04 1.10975246 Host Marine none 0 0.514915345 2.15E-04 0 Host Marine Soil 0 0.772373018 3.22E-04 0 Host Soil Host Soil 10 4.022776135 0.001679656 2.485845511 Host Soil Marine 15 22.52754636 0.009406074 0.665851476 Host Soil none 15 12.87288363 0.005374899 1.165240084 Host Soil Soil 39 19.30932545 0.008062349 2.019749478 Marine Marine 64 31.5385649 0.013168503 2.029261642 Marine none 8 36.04407417 0.015049718 0.221950492 Marine Soil 10 54.06611126 0.022574577 0.184958743 none none 10 10.29830691 0.004299919 0.971033403 Soil none 35 30.89492072 0.012899758 1.132872303 Soil Soil 81 23.17119054 0.009674819 3.495720251 Table S4a. Frequency of intra-phylum and inter-phylum connections. A and B: phyla. Obs: observed number of connections. Exp: expected number of connections based on random selection. Prob: probability of this connection by chance. Ratio: Obs:Exp. Phylum A B Obs Exp Prob Ratio Actinobacteria Actinobacteria 116 19.84111532 0.003845923 5.846445532 Actinobacteria Apicomplexa 0 0.826713138 1.60E-04 0 Actinobacteria Bacteroidetes 0 14.05412335 0.002724195 0 Actinobacteria Chlorobi 0 6.613705106 0.001281974 0 Actinobacteria Chloroflexi 0 4.133565691 8.01E-04 0 Actinobacteria Crenarchaeota 0 1.653426276 3.20E-04 0 Actinobacteria Cyanobacteria 0 14.05412335 0.002724195 0 Actinobacteria Euryarchaeota 0 9.920557659 0.001922961 0 Actinobacteria Firmicutes 4 162.0357751 0.031408369 0.024685907 Actinobacteria Fusobacteria 0 2.480139415 4.81E-04 0 Actinobacteria Proteobacteria 24 370.3674859 0.071790557 0.064800505 Actinobacteria Spirochaetes 0 10.7472708 0.002083208 0 Actinobacteria Thermi 0 3.306852553 6.41E-04 0 Apicomplexa Apicomplexa 0 0.008611595 1.67E-06 0 Apicomplexa Bacteroidetes 0 0.292794236 5.68E-05 0 Apicomplexa Chlorobi 0 0.137785523 2.67E-05 0 Apicomplexa Chloroflexi 0 0.086115952 1.67E-05 0 Apicomplexa Crenarchaeota 0 0.034446381 6.68E-06 0 Apicomplexa Cyanobacteria 0 0.292794236 5.68E-05 0 Apicomplexa Euryarchaeota 0 0.206678285 4.01E-05 0 Apicomplexa Firmicutes 0 3.375745314 6.54E-04 0 Apicomplexa Fusobacteria 0 0.051669571 1.00E-05 0 Apicomplexa Proteobacteria 13 7.71598929 0.001495637 1.684813121 Apicomplexa Spirochaetes 0 0.223901475 4.34E-05 0 Apicomplexa Thermi 0 0.068892762 1.34E-05 0 Bacteroidetes Bacteroidetes 29 2.48875101 4.82E-04 11.65243123 Bacteroidetes Chlorobi 0 2.342353892 4.54E-04 0 Bacteroidetes Chloroflexi 0 1.463971182 2.84E-04 0 Bacteroidetes Crenarchaeota 0 0.585588473 1.14E-04 0 Bacteroidetes Cyanobacteria 0 4.97750202 9.65E-04 0 Bacteroidetes Euryarchaeota 0 3.513530837 6.81E-04 0 Bacteroidetes Firmicutes 0 57.38767035 0.011123797 0 Bacteroidetes Fusobacteria 0 0.878382709 1.70E-04 0 Bacteroidetes Proteobacteria 0 131.1718179 0.025425822 0 Bacteroidetes Spirochaetes 0 3.806325074 7.38E-04 0 Bacteroidetes Thermi 0 1.171176946 2.27E-04 0 Chlorobi Chlorobi 14 0.551142092 1.07E-04 25.40179783 Chlorobi Chloroflexi 0 0.688927615 1.34E-04 0 Chlorobi Crenarchaeota 0 0.275571046 5.34E-05 0 Chlorobi Cyanobacteria 0 2.342353892 4.54E-04 0 Chlorobi Euryarchaeota 0 1.653426276 3.20E-04 0 Chlorobi Firmicutes 0 27.00596252 0.005234728 0 Chlorobi Fusobacteria 0 0.413356569 8.01E-05 0 Chlorobi Proteobacteria 0 61.72791432 0.011965093 0 Chlorobi Spirochaetes 0 1.7912118 3.47E-04 0 Chlorobi Thermi 0 0.551142092 1.07E-04 0 Chloroflexi Chloroflexi 3 0.21528988 4.17E-05 13.93470052 Chloroflexi Crenarchaeota 0 0.172231904 3.34E-05 0 Chloroflexi Cyanobacteria 0 1.463971182 2.84E-04 0 Chloroflexi Euryarchaeota 0 1.033391423 2.00E-04 0 Chloroflexi Firmicutes 0 16.87872657 0.003271705 0 Chloroflexi Fusobacteria 0 0.258347856 5.01E-05 0 Chloroflexi Proteobacteria 0 38.57994645 0.007478183 0 Chloroflexi Spirochaetes 0 1.119507375 2.17E-04 0 Chloroflexi Thermi 0 0.344463808 6.68E-05 0 Crenarchaeota Crenarchaeota 1 0.034446381 6.68E-06 29.03062609 Crenarchaeota Cyanobacteria 0 0.585588473 1.14E-04 0 Crenarchaeota Euryarchaeota 0 0.413356569 8.01E-05 0 Crenarchaeota Firmicutes 0 6.751490629 0.001308682 0 Crenarchaeota Fusobacteria 0 0.103339142 2.00E-05 0 Crenarchaeota Proteobacteria 0 15.43197858 0.002991273 0 Crenarchaeota Spirochaetes 0 0.44780295 8.68E-05 0 Crenarchaeota Thermi 0 0.137785523 2.67E-05 0 Cyanobacteria Cyanobacteria 19 2.48875101 4.82E-04 7.634351498 Cyanobacteria Euryarchaeota 0 3.513530837 6.81E-04 0 Cyanobacteria Firmicutes 1 57.38767035 0.011123797 0.017425346 Cyanobacteria Fusobacteria 0 0.878382709 1.70E-04 0 Cyanobacteria Proteobacteria 19 131.1718179 0.025425822 0.144848187 Cyanobacteria Spirochaetes 0 3.806325074 7.38E-04 0 Cyanobacteria Thermi 0 1.171176946 2.27E-04 0 Euryarchaeota Euryarchaeota 14 1.240069707 2.40E-04 11.28968792 Euryarchaeota Firmicutes 0 40.50894377 0.007852092 0 Euryarchaeota Fusobacteria 0 0.620034854 1.20E-04 0 Euryarchaeota Proteobacteria 0 92.59187148 0.017947639 0 Euryarchaeota Spirochaetes 0 2.686817699 5.21E-04 0 Euryarchaeota Thermi 0 0.826713138 1.60E-04 0 Firmicutes Firmicutes 1043 330.8230408 0.06412542 3.152742921 Firmicutes Fusobacteria 2 10.12723594 0.001963023 0.197487252 Firmicutes Proteobacteria 385 1512.333901 0.293144776 0.254573411 Firmicutes Spirochaetes 0 43.88468909 0.008506433 0 Firmicutes Thermi 0 13.50298126 0.002617364 0 Fusobacteria Fusobacteria 3 0.077504357 1.50E-05 38.70750145 Fusobacteria Proteobacteria 0 23.14796787 0.00448691 0 Fusobacteria Spirochaetes 0 0.671704425 1.30E-04 0 Fusobacteria Thermi 0 0.206678285 4.01E-05 0 Proteobacteria Proteobacteria 3450 1728.381601 0.335022601 1.996086974 Proteobacteria Spirochaetes 0 100.3078608 0.019443276 0 Proteobacteria Thermi 0 30.86395716 0.005982546 0 Spirochaetes Spirochaetes 17 1.455359587 2.82E-04 11.68096198 Spirochaetes Thermi 0 0.8956059 1.74E-04 0 Thermi Thermi 2 0.137785523 2.67E-05 14.51531305 Table S4b. Identical to Table S4a, but at a 90% cutoff level. This table serves as a control to verify that the signal is also present when cutoff levels are increased. Phylum 90% A B obs exp prob ratio Actinobacteria Actinobacteria 44 5.046170384 0.00210696 8.719483618 Actinobacteria Apicomplexa 0 0.360440742 1.50E-04 0 Actinobacteria Bacteroidetes 0 3.964848159 0.001655469 0 Actinobacteria Chlorobi 0 2.16264445 9.03E-04 0 Actinobacteria Chloroflexi 0 0 0 0 Actinobacteria Crenarchaeota 0 0 0 0 Actinobacteria Cyanobacteria 0 1.802203709 7.52E-04 0 Actinobacteria Euryarchaeota 0 2.883525934 0.001203977 0 Actinobacteria Firmicutes 0 58.7518409 0.02453104 0 Actinobacteria Fusobacteria 0 1.081322225 4.51E-04 0 Actinobacteria Proteobacteria 21 133.3630744 0.055683956 0.157464876 Actinobacteria Spirochaetes 0 4.685729643 0.001956463 0 Actinobacteria Thermi 0 0.720881483 3.01E-04 0 Apicomplexa Apicomplexa 0 0.006436442 2.69E-06 0 Apicomplexa Bacteroidetes 0 0.14160172 5.91E-05 0 Apicomplexa Chlorobi 0 0.077237302 3.22E-05 0 Apicomplexa Chloroflexi 0 0 0 0 Apicomplexa Crenarchaeota 0 0 0 0 Apicomplexa Cyanobacteria 0 0.064364418 2.69E-05 0 Apicomplexa Euryarchaeota 0 0.102983069 4.30E-05 0 Apicomplexa Firmicutes 0 2.098280032 8.76E-04 0 Apicomplexa Fusobacteria 0 0.038618651 1.61E-05 0 Apicomplexa Proteobacteria 1 4.762966944 0.001988713 0.209953168 Apicomplexa Spirochaetes 0 0.167347487 6.99E-05 0 Apicomplexa Thermi 0 0.025745767 1.07E-05 0 Bacteroidetes Bacteroidetes 19 0.77880946 3.25E-04 24.39621111 Bacteroidetes Chlorobi 0 0.84961032 3.55E-04 0 Bacteroidetes Chloroflexi 0 0 0 0 Bacteroidetes Crenarchaeota 0 0 0 0 Bacteroidetes Cyanobacteria 0 0.7080086 2.96E-04 0 Bacteroidetes Euryarchaeota 0 1.13281376 4.73E-04 0 Bacteroidetes Firmicutes 0 23.08108035 0.009637194 0 Bacteroidetes Fusobacteria 0 0.42480516 1.77E-04 0 Bacteroidetes Proteobacteria 0 52.39263639 0.02187584 0 Bacteroidetes Spirochaetes 0 1.84082236 7.69E-04 0 Bacteroidetes Thermi 0 0.28320344 1.18E-04 0 Chlorobi Chlorobi 4 0.231711905 9.67E-05 17.26281605 Chlorobi Chloroflexi 0 0 0 0 Chlorobi Crenarchaeota 0 0 0 0 Chlorobi Cyanobacteria 0 0.386186509 1.61E-04 0 Chlorobi Euryarchaeota 0 0.617898414 2.58E-04 0 Chlorobi Firmicutes 0 12.58968019 0.005256651 0 Chlorobi Fusobacteria 0 0.231711905 9.67E-05 0 Chlorobi Proteobacteria 0 28.57780167 0.011932276 0 Chlorobi Spirochaetes 0 1.004084923 4.19E-04 0 Chlorobi Thermi 0 0.154474604 6.45E-05 0 Chloroflexi Chloroflexi 0 0 0 0 Chloroflexi Crenarchaeota 0 0 0 0 Chloroflexi Cyanobacteria 0 0 0 0 Chloroflexi Euryarchaeota 0 0 0 0 Chloroflexi Firmicutes 0 0 0 0 Chloroflexi Fusobacteria 0 0 0 0 Chloroflexi Proteobacteria 0 0 0 0 Chloroflexi Spirochaetes 0 0 0 0 Chloroflexi Thermi 0 0 0 0 Crenarchaeota Crenarchaeota 0 0 0 0 Crenarchaeota Cyanobacteria 0 0 0 0 Crenarchaeota Euryarchaeota 0 0 0 0 Crenarchaeota Firmicutes 0 0 0 0 Crenarchaeota Fusobacteria 0 0 0 0 Crenarchaeota Proteobacteria 0 0 0 0 Crenarchaeota Spirochaetes 0 0 0 0 Crenarchaeota Thermi 0 0 0 0 Cyanobacteria Cyanobacteria 3 0.160911045 6.72E-05 18.64384134 Cyanobacteria Euryarchaeota 0 0.514915345 2.15E-04 0 Cyanobacteria Firmicutes 0 10.49140016 0.004380543 0 Cyanobacteria Fusobacteria 0 0.193093255 8.06E-05 0 Cyanobacteria Proteobacteria 11 23.81483472 0.009943564 0.46189697 Cyanobacteria Spirochaetes 0 0.836737436 3.49E-04 0 Cyanobacteria Thermi 0 0.128728836 5.37E-05 0 Euryarchaeota Euryarchaeota 5 0.411932276 1.72E-04 12.13791754 Euryarchaeota Firmicutes 0 16.78624026 0.007008869 0 Euryarchaeota Fusobacteria 0 0.308949207 1.29E-04 0 Euryarchaeota Proteobacteria 0 38.10373555 0.015909702 0 Euryarchaeota Spirochaetes 0 1.338779898 5.59E-04 0 Euryarchaeota Thermi 0 0.205966138 8.60E-05 0 Firmicutes Firmicutes 542 171.0098226 0.071402849 3.169408585 Firmicutes Fusobacteria 0 6.294840097 0.002628326 0 Firmicutes Proteobacteria 329 776.3636119 0.324160172 0.423770505 Firmicutes Spirochaetes 0 27.27764042 0.011389411 0 Firmicutes Thermi 0 4.196560064 0.001752217 0 Fusobacteria Fusobacteria 3 0.057927976 2.42E-05 51.78844816 Fusobacteria Proteobacteria 0 14.28890083 0.005966138 0 Fusobacteria Spirochaetes 0 0.502042462 2.10E-04 0 Fusobacteria Thermi 0 0.077237302 3.22E-05 0 Proteobacteria Proteobacteria 1403 881.1488847 0.367911852 1.592239432 Proteobacteria Spirochaetes 0 61.91857028 0.025853265 0 Proteobacteria Thermi 0 9.525933889 0.003977425 0 Spirochaetes Spirochaetes 9 1.087758667 4.54E-04 8.273894084 Spirochaetes Thermi 0 0.334694974 1.40E-04 0 Thermi Thermi 1 0.025745767 1.07E-05 38.84133612 Table S5: The top 30 network microbes ranked by their two-path scores. Rank IMG Identifier Species Phylum Habitat Score 1 637000016 Bacillus cereus ATCC 10987 Firmicutes Soil 2784 2 640963051 Streptococcus pneumoniae SP19-BS75 Firmicutes Host 1204 3 640069307 Burkholderia vietnamiensis G4 Proteobacteria Soil 908 4 638341239 Yersinia frederiksenii ATCC 33641 Proteobacteria Host 828 5 637000279 Staphylococcus aureus subsp. aureus NCTC 8325 Firmicutes Host 672 6 638341087 Escherichia coli E22 Proteobacteria Host 658 7 637000231 Ralstonia solanacearum GMI1000 Proteobacteria Soil 630 8 638341196 Shigella dysenteriae 1012 Proteobacteria Host 564 9 638341243 Yersinia pestis biovar Orientalis str. IP275 Proteobacteria Host 526 10 640753023 Escherichia coli APEC O1 Proteobacteria Host 476 11 639633059 Shewanella sp. W3-18-1 Proteobacteria Marine 422 12 640196205 Shewanella putrefaciens 200 Proteobacteria Aquatic Soil 414 13 638341151 Photobacterium sp. SKA34 Proteobacteria Marine 404 14 638341168 Ralstonia solanacearum UW551 Proteobacteria Soil 382 15 638341205 Streptococcus agalactiae COH1 Firmicutes Host 360 16 639857024 Clostridium cellulolyticum H10 Firmicutes Soil 356 17 641736232 Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 Proteobacteria Aquatic Host Soil 354 18 639633003 Acidovorax sp. JS42 Proteobacteria Soil 354 19 641522624 Escherichia coli SMS-3-5 Proteobacteria Host 344 20 639633058 Shewanella sp. ANA-3 Proteobacteria Host Soil 282 21 641380428 Clostridium bolteae ATCC BAA-613 Firmicutes Host 272 22 640753042 Pseudomonas aeruginosa PA7 Proteobacteria Aquatic Host Soil 270 23 641736234 Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 Proteobacteria Aquatic Host Soil 250 24 641228508 Shewanella pealeana ATCC 700345 Proteobacteria Host 246 25 637000254 Salmonella enterica subsp. enterica serovar Typhi str. CT18 Proteobacteria Aquatic Host Soil 242 26 641228479 Bordetella petrii Proteobacteria Aquatic 234 27 637000230 Ralstonia metallidurans CH34 Proteobacteria Aquatic Soil 226 28 641736208 Salmonella enterica subsp. enterica serovar Hadar str. RI_05P066 Proteobacteria Aquatic Host Soil 224 29 640753038 Ochrobactrum anthropi ATCC 49188 Proteobacteria Host Soil 218 30 640753032 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Proteobacteria Aquatic Host Soil 204 Table S6: Effect of collapsing nodes by genus. Here, genomes in the same genus and habitat were represented by a single member. Results are largely consistent with Table S3a. eco1 eco2 obs exp prob ratio Aquatic Aquatic 36 20.33103484 0.010883852 1.770691963 Aquatic Aquatic Host 3 7.934062377 0.004247357 0.378116513 Aquatic Aquatic Host Soil 15 18.84339814 0.010087472 0.796034764 Aquatic Aquatic Marine 11 6.94230458 0.003716437 1.584488245 Aquatic Aquatic Marine Soil 3 1.983515594 0.001061839 1.512466052 Aquatic Aquatic Soil 10 17.85164035 0.009556553 0.560172612 Aquatic Host 33 135.8708182 0.072735984 0.24287776 Aquatic Host Marine 0 0.991757797 5.31E-04 0 Aquatic Host Soil 24 18.84339814 0.010087472 1.273655623 Aquatic Marine 72 56.53019443 0.030262417 1.273655623 Aquatic none 29 35.70328069 0.019113105 0.812250287 Aquatic Soil 27 47.60437426 0.02548414 0.56717477 Aquatic Host Aquatic Host 4 0.774054866 4.14E-04 5.167592345 Aquatic Host Aquatic Host Soil 3 3.676760614 0.001968287 0.815935633 Aquatic Host Aquatic Marine 4 1.354596016 7.25E-04 2.952909911 Aquatic Host Aquatic Marine Soil 1 0.387027433 2.07E-04 2.583796172 Aquatic Host Aquatic Soil 2 3.483246897 0.001864693 0.574176927 Aquatic Host Host 12 26.51137916 0.014192387 0.452635826 Aquatic Host Host Marine 0 0.193513717 1.04E-04 0 Aquatic Host Host Soil 3 3.676760614 0.001968287 0.815935633 Aquatic Host Marine 11 11.03028184 0.005904862 0.997254663 Aquatic Host none 2 6.966493794 0.003729386 0.287088464 Aquatic Host Soil 3 9.288658392 0.004972515 0.322974522 Aquatic Host Soil Aquatic Host Soil 17 4.366153229 0.002337341 3.893587584 Aquatic Host Soil Aquatic Marine 6 3.217165537 0.001722251 1.864995733 Aquatic Host Soil Aquatic Marine Soil 0 0.919190153 4.92E-04 0 Aquatic Host Soil Aquatic Soil 7 8.27271138 0.004428646 0.846155472 Aquatic Host Soil Host 109 62.96452551 0.033706919 1.731133509 Aquatic Host Soil Host Marine 0 0.459595077 2.46E-04 0 Aquatic Host Soil Host Soil 26 8.732306457 0.004674682 2.977449329 Aquatic Host Soil Marine 19 26.19691937 0.014024047 0.725276119 Aquatic Host Soil none 18 16.54542276 0.008857293 1.087914178 Aquatic Host Soil Soil 30 22.06056368 0.011809724 1.359892722 Aquatic Marine Aquatic Marine 1 0.592635757 3.17E-04 1.687377092 Aquatic Marine Aquatic Marine Soil 1 0.338649004 1.81E-04 2.952909911 Aquatic Marine Aquatic Soil 3 3.047841035 0.001631607 0.984303304 Aquatic Marine Host 13 23.19745677 0.012418339 0.560406261 Aquatic Marine Host Marine 0 0.169324502 9.06E-05 0 Aquatic Marine Host Soil 5 3.217165537 0.001722251 1.554163111 Aquatic Marine Marine 24 9.651496611 0.005166754 2.486660978 Aquatic Marine none 5 6.09568207 0.003263213 0.820252753 Aquatic Marine Soil 4 8.127576093 0.004350951 0.492151652 Aquatic Marine Soil Aquatic Marine Soil 0 0.048378429 2.59E-05 0 Aquatic Marine Soil Aquatic Soil 2 0.870811724 4.66E-04 2.296707709 Aquatic Marine Soil Host 7 6.62784479 0.003548097 1.05615026 Aquatic Marine Soil Host Marine 0 0.048378429 2.59E-05 0 Aquatic Marine Soil Host Soil 2 0.919190153 4.92E-04 2.175828356 Aquatic Marine Soil Marine 6 2.75757046 0.001476215 2.175828356 Aquatic Marine Soil none 3 1.741623449 9.32E-04 1.722530782 Aquatic Marine Soil Soil 4 2.322164598 0.001243129 1.722530782 Aquatic Soil Aquatic Soil 3 3.918652759 0.00209778 0.765569236 Aquatic Soil Host 57 59.65060311 0.031932871 0.955564521 Aquatic Soil Host Marine 0 0.435405862 2.33E-04 0 Aquatic Soil Host Soil 16 8.27271138 0.004428646 1.934069649 Aquatic Soil Marine 27 24.81813414 0.013285939 1.087914178 Aquatic Soil none 16 15.67461104 0.008391119 1.020758982 Aquatic Soil Soil 35 20.89948138 0.011188159 1.674682704 Host Host 342 227.0036841 0.121522315 1.506583479 Host Host Marine 0 3.313922395 0.001774048 0 Host Host Soil 57 62.96452551 0.033706919 0.905271652 Host Marine 82 188.8935765 0.101120758 0.434106874 Host none 100 119.3012062 0.063865742 0.838214492 Host Soil 156 159.068275 0.085154323 0.980710956 Host Marine Host Marine 0 0.012094607 6.47E-06 0 Host Marine Host Soil 0 0.459595077 2.46E-04 0 Host Marine Marine 3 1.37878523 7.38E-04 2.175828356 Host Marine none 0 0.870811724 4.66E-04 0 Host Marine Soil 0 1.161082299 6.22E-04 0 Host Soil Host Soil 11 4.366153229 0.002337341 2.519380201 Host Soil Marine 26 26.19691937 0.014024047 0.99248311 Host Soil none 24 16.54542276 0.008857293 1.450552237 Host Soil Soil 38 22.06056368 0.011809724 1.722530782 Marine Marine 96 39.29537906 0.02103607 2.443035347 Marine none 29 49.63626828 0.026571878 0.584250207 Marine Soil 35 66.18169104 0.035429171 0.52884717 none none 13 15.67461104 0.008391119 0.829366673 Soil none 40 41.79896276 0.022376318 0.956961545 Soil Soil 42 27.86597518 0.014917546 1.507214434