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Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis

OTU Log2 (FC CD / FDR Adjusted Class Order Family Species Number Control) p value

518372 Clostridiales prausnitzii 2.16 5.69E-08 194497 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 8.93E-06 175761 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 5.74 1.99E-05 193709 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.40 2.14E-05 4464079 Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 7.79 0.000123188 20421 Firmicutes Clostridia Clostridiales NA 1.19 0.00013719 3044876 Firmicutes Clostridia Clostridiales Lachnospiraceae [] gnavus -4.32 0.000194983 184000 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.81 0.000306032 4392484 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 5.53 0.000339948 528715 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.17 0.000722263 186707 Firmicutes Clostridia Clostridiales NA NA NA 2.28 0.001028539 193101 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.90 0.001230738 339685 Firmicutes Clostridia Clostridiales NA 3.52 0.001382447 101237 Firmicutes Clostridia Clostridiales NA NA NA 2.64 0.001415109 347690 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 3.18 0.00152075 2110315 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.47 0.001609606 185068 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.67 0.001632 890882 Actinobacteria Actinomycetales Actinomycetaceae Actinomyces NA -2.95 0.00165125 4474255 Betaproteobacteria Burkholderiales Alcaligenaceae Sutterella NA 2.03 0.001857837 176868 Firmicutes Clostridia Clostridiales Dehalobacteriaceae Dehalobacterium NA -1.02 0.002146762 4329132 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA -3.59 0.002482182 182089 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.94 0.002587873 186248 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.98 0.002636611 530327 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.86 0.002728229 184420 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 1.23 0.002826497 4375889 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.57 0.002826497 4446902 Firmicutes Gemellales Gemellaceae NA NA -2.73 0.002864017 185088 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus 1.55 0.002866554 4457872 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 4.49 0.00300482 3443092 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.82 0.003054182 184249 Firmicutes Clostridia Clostridiales NA NA NA 2.24 0.003098819 175545 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.51 0.003303848 183532 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.05 0.003344644 174270 Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia NA 3.89 0.003353554 4450214 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 3.54 0.004043323 175397 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 2.06 0.004452497 177732 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.32 0.004475797 3232397 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae NA NA -1.46 0.004801527 732765 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 4.64 0.004883684 910500 Firmicutes Bacilli Lactobacillales NA -2.42 0.005188952 355355 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.60 0.006400429 4453304 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 4.24 0.006574081 185001 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 2.44 0.006824993 4454068 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Serratia NA -1.83 0.007027138 4324240 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.97 0.007198793 4472174 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] NA 1.38 0.007259662 246937 Firmicutes Clostridia Clostridiales NA NA NA -2.43 0.007360569 4413347 Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium NA 2.85 0.007789277 195120 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 1.49 0.007847919 4429536 Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia producta -4.67 0.008134399 192228 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 1.74 0.008506686 4464473 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -2.92 0.008546401 189142 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.12 0.008810268 304641 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae NA NA -1.89 0.009101771 1972262 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 3.15 0.009283961 4381338 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] torques 2.26 0.009454436 4368754 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 4.90 0.009474286 180182 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.32 0.009735305 178420 Firmicutes Clostridia Clostridiales NA NA NA 3.54 0.009923018 1028632 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae NA NA -2.36 0.010128511 3768338 Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia NA -1.96 0.011179678 3449122 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus NA -2.22 0.011250349 181931 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.81 0.011297621 304242 Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus NA 1.69 0.011322368 4474380 Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia NA -4.55 0.012659454 911422 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus NA -1.89 0.01327303 2877100 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.10 0.013302828 1775194 Firmicutes Clostridia Clostridiales NA NA NA 2.54 0.013472813 520774 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.15 0.013542622 3123133 Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Sutterella NA -4.49 0.013550376 1694319 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.88 0.013840043 194648 Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia NA 2.12 0.014172163 175717 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA -3.40 0.01450776 197988 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 1.75 0.015245336 178980 Firmicutes Clostridia Clostridiales NA NA 1.93 0.015440895 Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis

OTU Log2 (FC CD / FDR Adjusted Phylum Class Order Family Genus Species Number Control) p value

168071 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 2.48 0.016145264 3124103 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] NA 1.28 0.016159928 164304 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae NA NA -1.90 0.016724781 859619 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 2.30 0.017807567 189478 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 1.06 0.018531906 193644 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA -3.48 0.018531906 354461 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.87 0.0185407 192461 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 1.41 0.018665683 189356 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 0.018742581 181160 Firmicutes Clostridia Clostridiales Clostridiaceae NA -1.91 0.020235235 1015007 Proteobacteria Betaproteobacteria Rhodocyclales Rhodocyclaceae Methyloversatilis NA -1.62 0.020607857 361581 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.00 0.020754035 184309 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.98 0.021068608 4343184 Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA 3.31 0.02120183 173135 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 3.30 0.023122366 923098 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus NA -1.98 0.023371487 4404224 Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella copri -2.93 0.024275624 4429986 Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Sutterella NA 3.84 0.02512309 4386814 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.65 0.026009991 965141 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus NA -2.76 0.026009991 1144463 Firmicutes Clostridia Clostridiales Veillonella NA -1.88 0.026264632 4357222 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides ovatus -1.42 0.02730158 750031 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae NA NA -1.48 0.028482966 4394763 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -2.00 0.029415163 102910 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.51 0.029638154 2642538 Bacteroidetes Bacteroidia Bacteroidales [Odoribacteraceae] Odoribacter NA -3.54 0.02991114 192071 Firmicutes Clostridia Clostridiales Lachnospiraceae NA 3.09 0.029948719 4356466 Firmicutes Clostridia Clostridiales NA NA NA 1.95 0.030748938 183681 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.10 0.031069242 178342 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.25 0.031631507 3141094 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 3.59 0.032964117 1016923 Firmicutes Bacilli NA NA -1.86 0.034959969 356760 Firmicutes Erysipelotrichi Erysipelotrichales NA NA -3.38 0.038251995 4381430 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.56 0.039425375 195933 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 2.47 0.040569543 4338116 Firmicutes Clostridia Clostridiales NA NA NA 4.48 0.040603514 845272 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 1.56 0.0406656 535353 Firmicutes Bacilli Gemellales Gemellaceae NA NA -1.92 0.041945653 3440955 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Proteus NA -1.32 0.043652844 526358 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 1.67 0.044004858 247639 Firmicutes Clostridia Clostridiales Clostridiaceae SMB53 NA -3.51 0.047489586 317533 Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium NA 1.86 0.049324985