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Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In

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Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In Table S8. Species identified by random forests analysis of shotgun sequencing data that exhibit significant differences in their representation in the fecal microbiomes between each two groups of mice. (a) Species discriminating fecal microbiota of the Soil and Control mice. Mean importance of species identified by random forest are shown in the 5th column. Random forests assigns an importance score to each species by estimating the increase in error caused by removing that species from the set of predictors. In our analysis, we considered a species to be “highly predictive” if its importance score was at least 0.001. T-test was performed for the relative abundances of each species between the two groups of mice. P-values were at least 0.05 to be considered statistically significant. Microbiological Taxonomy Random Forests Mean of relative abundance P-Value Species Microbiological Function (T-Test) Classification Bacterial Order Importance Score Soil Control Rhodococcus sp. 2G Engineered strain Bacteria Corynebacteriales 0.002 5.73791E-05 1.9325E-05 9.3737E-06 Herminiimonas arsenitoxidans Engineered strain Bacteria Burkholderiales 0.002 0.005112829 7.1580E-05 1.3995E-05 Aspergillus ibericus Engineered strain Fungi 0.002 0.001061181 9.2368E-05 7.3057E-05 Dichomitus squalens Engineered strain Fungi 0.002 0.018887472 8.0887E-05 4.1254E-05 Acinetobacter sp. TTH0-4 Engineered strain Bacteria Pseudomonadales 0.001333333 0.025523638 2.2311E-05 8.2612E-06 Rhizobium tropici Engineered strain Bacteria Rhizobiales 0.001333333 0.02079554 7.0081E-05 4.2000E-05 Methylocystis bryophila Engineered strain Bacteria Rhizobiales 0.001333333 0.006513543 3.5401E-05 2.2044E-05 Alteromonas naphthalenivorans Engineered strain Bacteria Alteromonadales 0.001 0.000660472 2.0747E-05 4.6463E-05 Saccharomyces cerevisiae Engineered strain Fungi 0.001 0.002980726 3.9901E-05 7.3043E-05 Bacillus phage Belinda Antibiotic Phage 0.002 0.016409765 6.8789E-07 6.0681E-08 Streptomyces sp. Mg1 Antibiotic Bacteria Streptomycetaceae 0.001333333 0.025944045 1.0137E-04 5.0762E-05 Streptosporangium sp. Antibiotic Bacteria Streptosporangiales 0.001333333 0.005225191 1.4746E-04 6.8699E-05 Pseudomonas sp. Os17 Antibiotic Bacteria Pseudomonadales 0.001333333 0.019992445 4.0231E-05 1.3165E-05 Acanthamoeba castellanii Antibiotic Fungi 0.001 0.002183997 1.9172E-04 1.2956E-04 Pseudoalteromonas luteoviolacea Antibiotic Bacteria Alteromonadales 0.001333333 0.004368358 5.4894E-05 8.6223E-05 Pseudoalteromonas piscicida Antibiotic Bacteria Alteromonadales 0.001333333 0.003338405 4.6886E-05 8.2059E-05 Lactobacillus fermentum Antibiotic Bacteria Lactobacillales 0.001 0.025570099 1.9693E-04 4.6536E-04 Burkholderia sp. JP2-270 Antibiotic Bacteria Burkholderiales 0.001 0.001144007 4.0309E-05 9.2851E-05 Tetrapisispora phaffii Antibiotic Fungi 0.001 0.021789983 1.0335E-04 1.7016E-04 Legionella anisa Pathogany (no infecting mice) Bacteria Legionellales 0.002333333 0.003555933 4.0114E-05 1.3879E-05 Scale drop disease virus Pathogany (no infecting mice) Bacteria 0.002333333 0.047897164 3.2350E-06 0.0000E+00 Bordetella avium Pathogany (no infecting mice) Bacteria Burkholderiales 0.002 0.004001233 5.7584E-05 3.0745E-05 Staphylococcus condimenti Pathogany (no infecting mice) Bacteria Bacillales 0.001333333 0.013666952 3.3692E-05 1.4869E-05 Tropheryma whipplei Pathogany (no infecting mice) Bacteria Micrococcales 0.001333333 0.000588819 1.5019E-05 6.5443E-06 Rahnella aquatilis Pathogany (no infecting mice) Bacteria Enterobacterales 0.001333333 0.029064014 6.8549E-05 4.3551E-05 Brucella abortus Pathogany (no infecting mice) Bacteria Rhizobiales 0.001333333 0.004137196 8.4396E-06 1.1050E-06 Borrelia duttonii Pathogany (no infecting mice) Bacteria Borreliaceae 0.001333333 0.002099125 3.3756E-05 1.2974E-05 Macrococcus canis Pathogany (no infecting mice) Bacteria Bacillales 0.001 0.000562255 3.6211E-05 1.5288E-05 Mycobacterium ulcerans Pathogany (no infecting mice) Bacteria Corynebacteriales 0.001 0.003869858 1.0380E-05 2.0078E-06 Salmonella enterica Pathogany (no infecting mice) Bacteria Enterobacterales 0.001 0.010304803 3.4115E-03 2.3240E-03 Lelliottia amnigena Pathogany (no infecting mice) Bacteria Enterobacterales 0.001 0.019044704 7.0061E-05 3.6456E-05 Pseudomonas oryzihabitans Pathogany (no infecting mice) Bacteria Pseudomonadales 0.001 0.002847013 2.8164E-05 2.0365E-05 Ralstonia insidiosa Pathogany (no infecting mice) Bacteria Burkholderiales 0.001 0.001367639 1.0216E-04 5.8764E-05 Parachlamydia acanthamoebae Pathogany (no infecting mice) Chlamydia 0.001 0.000544995 2.4367E-05 1.5029E-05 Leptospira alstonii Pathogany (no infecting mice) Bacteria Leptospiraceae 0.001 0.000830812 4.9841E-05 3.3563E-05 Plasmodium vinckei Pathogany (no infecting mice) Parasite 0.001 0.024245509 8.1069E-05 5.9239E-05 Cryptococcus neoformans Pathogany (no infecting mice) Fungi 0.001 0.00096144 1.0665E-04 4.5948E-05 Leptospira borgpetersenii Pathogany (infecting mice) Bacteria Legionellales 0.002333333 0.014135181 6.2940E-05 3.1533E-05 Mycoplasma penetrans Pathogany (infecting mice) Mycoplasma 0.0018 0.014209115 2.4312E-05 1.5115E-05 Paracoccidioides brasiliensis Pathogany (infecting mice) Fungi 0.001 0.000499713 7.2846E-05 4.3384E-05 Rhodobacter capsulatus Unreported Bacteria Rhodobacterales 0.001333333 0.001634871 1.2132E-04 4.4714E-05 Acetobacter tropicalis Unreported Bacteria Rhodospirillales 0.001333333 0.002692973 2.9932E-05 1.5084E-05 Cellulophaga phage phi19:1 Unreported Virus 0.003333333 0.008122172 5.1419E-06 7.1203E-07 Tessaracoccus aquimaris Unreported Bacteria Propionibacteriales 0.002933333 0.000772982 1.5977E-04 8.0103E-05 Thermocrinis albus Unreported Bacteria Aquificales 0.002333333 0.001225119 3.2967E-05 7.3177E-06 halophilic archaeon DL31 Unreported Archaea 0.002333333 0.004364837 2.8682E-05 1.4195E-05 Streptomyces sp. GBA 94-10 Unreported Bacteria Streptomycetales 0.002 0.015059096 5.8274E-05 2.4043E-05 Chthonomonas calidirosea Unreported Bacteria Chthonomonadales 0.002 0.003175406 6.6221E-05 2.0497E-05 Lutibacter profundi Unreported Bacteria Flavobacteriales 0.002 0.012388797 6.9978E-05 4.4559E-05 Enterobacter cloacae complex sp. 35734 Unreported Bacteria Enterobacterales 0.002 0.025039797 5.0645E-05 8.4808E-06 Bathymodiolus septemdierum thioautotrophic gill symbiont Unreported Bacteria Gammaproteobacteria 0.002 8.12284E-05 1.9922E-05 1.1641E-05 Hammondia hammondi Unreported Parasite 0.002 0.01219127 1.8657E-04 1.1765E-04 Edwardsiella phage PEi20 Unreported Virus 0.002 0.005972022 1.3045E-05 7.4631E-07 Microbulbifer agarilyticus Unreported Bacteria Cellvibrionales 0.0016 6.71021E-05 3.6501E-05 2.2731E-05 Parvibaculum lavamentivorans Unreported Bacteria Rhizobiales 0.0016 0.005553949 1.0266E-04 6.3333E-05 Thielavia terrestris Unreported Fungi 0.001466667 0.03131429 1.2684E-04 8.9564E-05 Veillonella rodentium Unreported Bacteria Veillonellales 0.001333333 0.026301936 1.1501E-04 7.6491E-05 Mycobacterium sp. WY10 Unreported Bacteria Corynebacteriales 0.001333333 0.001679688 1.0795E-05 5.6407E-06 Aeromicrobium choanae Unreported Bacteria Propionibacteriales 0.001333333 0.001752489 4.6754E-05 2.8824E-05 Tenericutes bacterium MO-XQ Unreported Bacteria unclassified Tenericutes 0.001333333 0.010895761 8.5206E-05 5.8651E-05 Pseudomonas savastanoi Unreported Bacteria Pseudomonadales 0.001333333 0.000487371 1.2039E-05 3.7777E-06 Pseudomonas psychrotolerans Unreported Bacteria Pseudomonadales 0.001333333 0.010464629 3.3400E-05 2.0807E-05 Pseudomonas psychrophila Unreported Bacteria Pseudomonadales 0.001333333 0.00759328 2.4340E-05 1.1078E-05 Pseudomonas sp. PONIH3 Unreported Bacteria Pseudomonadales 0.001333333 0.004419775 4.5263E-05 1.4885E-05 Psychrobacter sp. PRwf-1 Unreported Bacteria Pseudomonadales 0.001333333 0.009784621 4.1590E-05 6.8389E-06 Stenotrophomonas sp. WZN-1 Unreported Bacteria Xanthomonadales 0.001333333 0.016570077 1.0117E-04 4.0934E-05 Alteromonas sp. RW2A1 Unreported Bacteria Alteromonadales 0.001333333 2.0299E-05 2.3511E-05 6.3903E-06 Sinorhizobium sp. CCBAU 05631 Unreported Bacteria Rhizobiales 0.001333333 0.003366292 1.2685E-05 5.0010E-06 Ensifer sojae Unreported Bacteria Rhizobiales 0.001333333 0.000235271 5.5267E-05 3.1256E-05 Bradyrhizobium sp. WSM471 Unreported Bacteria Rhizobiales 0.001333333 0.007090958 1.8885E-05 1.1666E-05 Rhodomicrobium vannielii Unreported Bacteria Rhizobiales 0.001333333 0.000845025 5.5689E-05 2.8716E-05 Rickettsia canadensis Unreported Bacteria Rickettsiales 0.001333333 0.010681269 1.0533E-05 3.4078E-06 Nitrosomonas communis Unreported Bacteria Nitrosomonadales 0.001333333 0.000127601 3.2601E-05 1.5366E-05 Methanobrevibacter millerae Unreported Archaea 0.001333333 0.008346112 4.9261E-05 2.0660E-05 Lactobacillus prophage Lj771 Unreported Virus 0.001333333 0.002946531 2.5356E-06 6.1759E-08 Beihai tombus-like virus 19 Unreported Virus 0.001333333 0.001201982 4.8762E-07 5.7830E-08 Bacillus sp. FJAT-22090 Unreported Bacteria Bacillales 0.001 0.027450499 1.1774E-04 4.9264E-05 Streptomyces sp. P3 Unreported Bacteria Streptomycetales 0.001 0.006365747 7.9812E-05 3.6799E-05 Mycobacteroides saopaulense Unreported Bacteria Corynebacteriales 0.001 0.044473572 2.9008E-05 1.7792E-05 Arthrobacter sp. Rue61a Unreported Bacteria Micrococcales 0.001 0.003741133 2.9955E-05 9.4745E-06 Synechococcus sp. SynAce01 Unreported Bacteria Synechococcales 0.001 0.015984543 6.7792E-05 2.9752E-05 Mesoplasma coleopterae Unreported Bacteria Entomoplasmatales 0.001 0.009546766 7.6010E-06 1.6952E-06 Deinococcus maricopensis Unreported Bacteria Deinococcales 0.001 0.001004967 6.9074E-05
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