Supplementary Table 1. Raw data from a 100% stacked bar chart showing microbiota analysis on the phylum level in 17 patients with UC at baseline (a), after combined antibiotic treatment (b), at 4 weeks after FMT (c), and for 17 individual donors (d).
donors
taxon 1d 2d 3d 4d 5d 6d 7d 8d 9d
Actinobacteria 23596 2170 2365 2181 3823 1988 3118 4348 4464
Aquificae 64 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 475201 70286 80884 59690 72576 68415 226746 114361 164367
Chlamydiae/Verrucomicrobia group 0 0 0 17056 0 538 0 396 115
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 537 0 65 56 0 0 333 205 239
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus-Thermus 0 0 0 0 0 66 110 0 143
Fibrobacteres/Acidobacteria group 0 0 0 0 0 0 96 191 214
Firmicutes 227774 164032 57500 114214 186195 182917 293905 289614 319795
Fusobacteria 4881 113 0 0 0 0 114 59 51
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 105 0 0 0 0 0 0 0 0
Opisthokonta 0 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0 0 0
Proteobacteria 78757 4124 6207 4269 29748 1809 43615 5963 7577
Spirochaetes 118 320 137 259 174 160 591 557 552
Synergistetes 0 0 0 0 0 0 0 167 90
Tenericutes 0 0 95 115 55 0 123 683 896
Thermotogae 135 52 0 0 66 82 82 177 89
Unclassified Bacteria 116606 36158 11830 23708 36474 45141 99663 44991 47529
Total reads 927774 277255 159083 221548 329111 301116 668496 461712 546121
Bacteroidetes% 51.219
5 25.350
7 50.843
9 26.942
2 22.052
1 22.720
5 33.918
8 24.768
9 30.097
2
Firmicutes% 24.550
6 59.162
9 36.144
7 51.552
7 56.575
1 60.746
4 43.965
1 62.726
1 58.557
5
Bacte+Firmi% 75.770
1 84.513
5 86.988
6
78.495 78.627 3
83.466 8
77.883 9 87.495
88.654 7
Bacte/Firmi% 2.0862 8
0.4284 9
1.4066 8
0.5226 2
0.3897 8
0.3740 2
0.7714 9
0.3948 7
0.5139 8
Proteo% 8.4888
1 1.4874
4 3.9017
4
1.9269 9.0389 0.6007 7
6.5243 5 1.2915
1.3874 2
donors
taxon 10d 11d 12d 13d 14d 15d 16d 17d
Actinobacteria 5721 3086 3499 2089 2218 4371 4322 1467
Aquificae 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 253994 275584 133925 124448 97412 75252 100623 46347
Chlamydiae/Verrucomicrobia group 382 0 143 0 0 64 0 0
Chloroflexi 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0
Cyanobacteria 0 251 187 168 51 282 0 177
Deferribacteres 0 0 0 0 0 0 0 0
Deinococcus-Thermus 121 220 0 0 63 0 0 94
Fibrobacteres/Acidobacteria group 134 0 116 53 0 0 0 92
Firmicutes 366582 425069 514557 577255 160195 138397 65952 406973
Fusobacteria 92 276 52 192 0 119 883 0
Gemmatimonadetes 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0 0
Opisthokonta 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0 0
Proteobacteria 28512 4381 19686 69606 20404 2041 19880 10005
Spirochaetes 699 561 571 519 131 182 0 76
Synergistetes 305 0 0 0 0 68 0 0
Tenericutes 226 81 185 153 0 0 0 0
Thermotogae 173 159 62 77 0 0 0 0
Unclassified Bacteria 79469 103851 107354 212750 90155 20879 49621 58035
Total reads 736410 813519 780337 987310 370629 241655 241281 523266
Bacteroidetes% 34.490
8 33.875
5 17.1625 12.604
8 26.2829 31.140
3 41.703
7 8.85725
Firmicutes% 49.779 52.250 65.9404 58.467 43.2225 57.270 27.334 77.7755
6 7 5 5 1
Bacte+Firmi% 84.270
4 86.126
2 83.1028 71.072
2 69.5054 88.410
8 69.037
8 86.6328
Bacte/Firmi% 0.6928
7 0.6483
3 0.26027 0.2155
9 0.60808 0.5437
4 1.5257 0.11388
Proteo% 3.8717
6 0.5385
2 2.52276 7.0500
7 5.50524 0.8445
9 8.2393
6 1.91203
patients with UC at baseline
taxon 1a 2a 3a 4a 5a 6a 7a 8a 9a
Actinobacteria 9273 1876 869 1587 1437 5483 4070 3246 3997
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 36833 540 93034 53667 174284 100034 135700 111159 127110
Chlamydiae/Verrucomicrobia group 0 0 0 11337 0 0 0 0 0
Chloroflexi 0 0 0 0 0 53 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 0 0 0 80 108 0 180 170 1035
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus-Thermus 0 0 0 0 73 94 99 0 98
Fibrobacteres/Acidobacteria group 0 0 0 0 0 0 0 61 0
Firmicutes 128338 235396 71910 78989 184577 163254 287138 350765 452795
Fusobacteria 77621 344 0 1421 2181 61 0 158 446
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0 0 62
Opisthokonta 0 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0 0 151
Proteobacteria 165202 5209 10380 1717 75333 53113 22972 16348 24123
Spirochaetes 87 465 229 284 316 215 398 448 681
Synergistetes 0 0 0 0 0 0 0 0 0
Tenericutes 0 90 0 128 59 0 64 181 0
Thermotogae 0 62 0 0 97 101 72 147 0
Unclassified Bacteria 114205 43843 41168 24142 34995 69145 92338 93084 27427
Total reads 531559 287825 217590 173352 473460 391553 543031 575767 637925
Bacteroidetes% 6.92924 0.18761 42.7566 30.9584 36.8107 25.548 24.9894 19.3062 19.9255
Firmicutes% 24.1437 81.7844 33.0484 45.5657 38.9847 41.694 52.8769 60.9213 70.9793
Bacte+Firmi% 31.0729 81.972 75.805 76.5241 75.7954 67.242 77.8663 80.2276 90.9049
Bacte/Firmi% 0.287 0.00229 1.29376 0.67942 0.94423 0.61275 0.4726 0.3169 0.28072
Proteo% 31.0788 1.80978 4.77044 0.99047 15.9112 13.5647 4.23033 2.83934 3.78148
patients with UC at baseline
taxon 10a 11a 12a 13a 14a 15a 16a 17a
Actinobacteria 5803 18651 5422 2883 2748 4199 7627 23771
Aquificae 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 133430 124196 34352 102926 64089 137548 15816 228279
Chlamydiae/Verrucomicrobia group 0 68 0 0 0 157 0 0
Chloroflexi 0 0 0 0 0 0 0 0
Chrysiogenetes 61 0 0 0 0 0 0 0
Cyanobacteria 160 312 0 62 0 732 0 151
Deferribacteres 82 0 0 0 0 0 0 0
Deinococcus-Thermus 0 287 0 56 0 73 0 81
Fibrobacteres/Acidobacteria group 100 0 0 0 0 118 0 0
Firmicutes 402879 376922 316900 292441 635091 415264 61501 200577
Fusobacteria 159 146 406 0 686 440 0 158
Gemmatimonadetes 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 138 0 0
Opisthokonta 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 103 0 0
Proteobacteria 41843 18698 9179 35192 604244 65234 2225 18574
Spirochaetes 700 712 368 264 737 176 0 104
Synergistetes 54 0 0 0 0 142 0 0
Tenericutes 300 151 0 53 0 955 0 62
Thermotogae 181 192 61 56 99 63 0 0
Unclassified Bacteria 69428 108981 39238 221846 171195 50516 12989 164248
Total reads 655180 649316 405926 655779 1478889 675858 100158 636005
Bacteroidetes% 20.3654 19.1272
8.4626
3 15.6952 4.33359 20.351
6 15.7911 35.8926
Firmicutes% 61.4913 58.0491
78.068
4 44.5944 42.9438 61.442
5 61.404 31.537
Bacte+Firmi% 81.8567 77.1763 86.531 60.2897 47.2774
81.794
1 77.195 67.4297
Bacte/Firmi% 0.33119 0.3295 0.1084 0.35195 0.10091
0.3312
3 0.25717 1.13811
Proteo% 6.38649 2.87965
2.2612
5 5.36644 40.858 9.6520
3 2.22149 2.92042
after combined antibiotic treatment
taxon 1b 2b 3b 4b 5b 6b 7b 8b 9b
Actinobacteria 12208 30661 818 1124 86 324 1064 1371 1502
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 2403 8536 0 435 74 121 340 657 2313
Chlamydiae/Verrucomicrobia group 0 0 0 0 0 0 0 0
Chloroflexi 3 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 88 0 0
Cyanobacteria 30 0 0 0 0 0 0 0 0
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus-Thermus 0 0 0 0 0 0 115 100 0
Fibrobacteres/Acidobacteria group 0 0 0 56 0 0 0 0 0
Firmicutes 2980 51737 12614 208581 5354 3224 55927 235736 117782
Fusobacteria 23 0 0 0 0 0 0 0 1731
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0 0 0
Opisthokonta 6 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0 0 0
Proteobacteria 290547 490822 291214 369065 116645 534859 661280 355969 380010
Spirochaetes 176 69 84 72 0 105 222 248 254
Synergistetes 0 0 0 245 0 0 0 0 0
Tenericutes 19 0 0 0 0 0 0 0 0
Thermotogae 14 0 0 0 0 0 0 0 0
Unclassified Bacteria 2578 8537 4400 8632 1125 7265 15011 6510 3174
Total reads 310987 590362 309130 588210 123284 545898 734047 600591 506766
Bacteroidetes% 0.7727 1.44589 0 0.07395 0.06002 0.02217 0.04632 0.10939 0.45642
Firmicutes% 0.95824 8.76361 4.08048 35.4603 4.34282 0.59059 7.61899 39.2507 23.2419
Bacte+Firmi% 1.73094 10.2095 4.08048 35.5342 4.40284 0.61275 7.66531 39.3601 23.6983
Bacte/Firmi% 0.80638 0.16499 0 0.00209 0.01382 0.03753 0.00608 0.00279 0.01964
Proteo% 93.4274 83.1392 94.2044 62.7437 94.6149 97.9778 90.0869 59.2698 74.9873
after combined antibiotic treatment
taxon 10b 11b 12b 13b 14b 15b 16b 17b
Actinobacteria 35926 989 5936 916 1005 853 148 2862
Aquificae 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 13074 464 5154 547 313 52 112 214
Chlamydiae/Verrucomicrobia group 0 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0 65
Chrysiogenetes 0 0 0 0 0 0 0 58
Cyanobacteria 369 0 126 0 0 0 0 0
Deferribacteres 0 0 0 0 0 0 0 0
Deinococcus-Thermus 507 0 0 0 0 0 0 727
Fibrobacteres/Acidobacteria group 148 0 0 0 0 0 0 0
Firmicutes 696810 35565 1026309 256811 135925 110589 1115 129797
Fusobacteria 91 0 0 0 0 0 0 0
Gemmatimonadetes 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0 0
Opisthokonta 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0 0
Proteobacteria 75707 595632 9083 1049904 8484 86920 436964 974598
Spirochaetes 971 141 736 255 77 90 0 0
Synergistetes 170 0 0 0 0 0 0 0
Tenericutes 553 0 89 0 0 0 0 677
Thermotogae 0 0 0 0 0 0 0 0
Unclassified Bacteria 9616 6753 5044 5342 579 1795 5796 21608
Total reads 833942 639544 1052477 1313775 146383 200299 444135 1130606
Bacteroidetes% 1.56773 0.07255 0.4897 0.04164 0.21382 0.02596 0.02522 0.01893
Firmicutes% 83.5562 5.56099 97.5137 19.5476 92.8557 55.212 0.25105 11.4803
Bacte+Firmi% 85.1239 5.63355 98.0034 19.5892 93.0696 55.2379 0.27627 11.4992
Bacte/Firmi% 0.01876 0.01305 0.00502 0.00213 0.0023 0.00047 0.10045 0.00165
Proteo% 9.07821 93.1339 0.86301 79.9151 5.79575 43.3951 98.3854 86.2014
at 4 weeks after FMT
taxon 1c 2c 3c 4c 5c 6c 7c 8c 9c
Actinobacteria 25627 4784 1210 1041 7308 15472 2769 6790 2246
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 5447 260 100344 99647 92149 80847 125250 224304 501
Chlamydiae/Verrucomicrobia group 0 0 0 9438 0 0 0 74 0
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 189
Cyanobacteria 0 0 0 95 0 0 403 581 138
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus-Thermus 0 0 0 0 76 0 0 128 349
Fibrobacteres/Acidobacteria group 0 0 0 0 0 0 0 161 0
Firmicutes 28616 115398 51334 78588 155798 190579 216161 643527 235912
Fusobacteria 121 115 0 1232 0 0 187 931 0
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0 59 0
Opisthokonta 0 0 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 69 0 0
Proteobacteria 853850 6767 25898 5491 111362 3159 8209 28620 1005814
Spirochaetes 99 267 173 203 166 138 409 966 397
Synergistetes 0 0 0 0 0 0 0 117 0
Tenericutes 0 81 67 0 0 0 82 582 0
Thermotogae 0 0 0 0 103 69 65 241 0
Unclassified Bacteria 9986 22599 17372 20578 75969 46064 56420 137172 22849
Total reads 923746 150271 196398 216313 442931 336328 410024 1044253 1268395
Bacteroidetes% 0.58966 0.17302 51.0922 46.0661 20.8044 24.0381 30.547 21.4799 0.0395
Firmicutes% 3.09782 76.7933 26.1377 36.3307 35.1743 56.6646 52.7191 61.6256 18.5993
Bacte+Firmi% 3.68749 76.9663 77.2299 82.3968 55.9787 80.7028 83.2661 83.1054 18.6388
Bacte/Firmi% 0.19035 0.00225 1.95473 1.26797 0.59146 0.42422 0.57943 0.34855 0.00212
Proteo% 92.4334 4.5032 13.1865 2.53845 25.1421 0.93926 2.00208 2.74072 79.2982
at 4 weeks after FMT
taxon 11c 12c 13c 14c 15c 16c 17c
Actinobacteria 2929 3231 1220 1330 16280 8370 1747
Aquificae 0 0 0 0 0 0 0
Bacteroidetes/Chlorobi group 201210 99333 33548 127711 117933 99031 124117
Chlamydiae/Verrucomicrobia group 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0
Cyanobacteria 86 56 0 70 251 103 110
Deferribacteres 0 0 0 0 0 0 0
Deinococcus-Thermus 102 0 0 54 0 0 50
Fibrobacteres/Acidobacteria group 0 75 0 0 0 0 99
Firmicutes 695368 493079 121689 152039 189694 353408 359113
Fusobacteria 414 203 0 342 92 144 0
Gemmatimonadetes 0 0 0 0 0 0 0
Nitrospirae 0 0 0 0 0 0 0
Opisthokonta 0 0 0 0 0 0 0
Planctomycetes 0 0 0 0 0 0 0
Proteobacteria 3067 10707 7989 36175 10794 8520 16905
Spirochaetes 590 455 53 126 268 70 69
Synergistetes 0 0 0 0 0 118 65
Tenericutes 291 124 0 50 102 73 115
Thermotogae 96 61 0 0 0 0 0
Unclassified Bacteria 192563 146871 44316 78579 32806 68788
Total reads 1096716 754195 208815 396476 368220 538625 605636
Bacteroidetes% 18.3466 13.1707 16.0659 32.2115 32.0279 18.3859 20.4937
Firmicutes% 63.4046 65.3782 58.276 38.3476 51.5165 65.613 59.2952
Bacte+Firmi% 81.7512 78.5489 74.3419 70.5591 83.5443 83.9989 79.7889
Bacte/Firmi% 0.28936 0.20145 0.27569 0.83999 0.6217 0.28022 0.34562
Proteo% 0.27965 1.41966 3.82587 9.12413 2.9314 1.58181 2.79128
Supplementary Table 1. Raw data from a 100% stacked bar chart showing microbiota analysis on the phylum level in four patients received only AFM therapy before undergoing AFM therapy, after AFM therapy, and at 4 weeks after AFM therapy.
patients with UC at baseline
taxon #A #B #C #D
Actinobacteria 1180 296 1076 433
Aquificae 0 0 0 0
Bacteroidetes/Chlorobi group 65389 51394 11756 17027
Chlamydiae/Verrucomicrobia group 0 0 0 0
Chloroflexi 0 0 0 0
Chrysiogenetes 0 0 0 0
Cyanobacteria 0 0 70 0
Deferribacteres 0 0 0 0
Deinococcus-Thermus 0 0 0 0
Fibrobacteres/Acidobacteria group 0 0 0 0
Firmicutes 193902 53843 109519 126502
Fusobacteria 0 9677 0 4302
Gemmatimonadetes 0 0 0 0
Nitrospirae 0 0 0 0
Opisthokonta 0 0 0 0
Planctomycetes 0 0 0 0
Proteobacteria 71964 40619 23497 7934
Spirochaetes 74 0 0 0
Synergistetes 0 0 0 0
Tenericutes 0 0 0 0
Thermotogae 0 0 0 0
Unclassified Bacteria 46437 38133 13141 23416
Total reads 378946 193962 159059 179614
Bacteroidetes% 17.2555 26.4969 7.39097 9.47977
Firmicutes% 51.1688 27.7596 68.8543 70.4299
Bacte+Firmi% 68.4243 54.2565 76.2453 79.9097
Bacte/Firmi% 33.7227 95.4516 10.7342 13.4599
Proteo% 18.9906 20.9417 14.7725 4.41725
after combined antibiotic treatment
taxon #A #B #C #D
Actinobacteria 176 219 1112 184
Aquificae 0 0 0 0
Bacteroidetes/Chlorobi group 55 96 0 0
Chlamydiae/Verrucomicrobia group 0 0 0 0
Chloroflexi 0 0 0 0
Chrysiogenetes 0 0 0 0
Cyanobacteria 0 0 0 0
Deferribacteres 0 0 0 0
Deinococcus-Thermus 0 0 0 0
Fibrobacteres/Acidobacteria group 0 0 0 0
Firmicutes 83851 20812 139494 61125
Fusobacteria 0 0 0 0
Gemmatimonadetes 0 0 0 0
Nitrospirae 0 0 0 0
Opisthokonta 0 0 0 0
Planctomycetes 0 0 0 0
Proteobacteria 159595 75332 21390 69563
Spirochaetes 108 0 0 0
Synergistetes 0 0 0 0
Tenericutes 0 0 0 0
Thermotogae 0 0 0 0
Unclassified Bacteria 2664 1208 1181 3026
Total reads 246449 97667 163177 133898
Bacteroidetes%
0.0223 2
0.0982
9 0 0
Firmicutes%
34.023 7
21.309 1
85.486 3
45.650 4
Bacte+Firmi% 34.046
21.407 4
85.486 3
45.650 4
Bacte/Firmi%
0.0655 9
0.4612
7 0 0
Proteo%
64.757 8
77.131 5
13.108 5
51.952 2
at 4 weeks after FMT
taxon #A #B #C #D
Actinobacteria 2504 197 345 151
Aquificae 0 0 0 0
Bacteroidetes/Chlorobi group 1334 434 8145 21579
Chlamydiae/Verrucomicrobia group 0 0 0 0
Chloroflexi 0 0 0 0
Chrysiogenetes 0 0 0 0
Cyanobacteria 164 0 0 0
Deferribacteres 0 0 0 0
Deinococcus-Thermus 100 0 0 0
Fibrobacteres/Acidobacteria group 0 0 0 0
Firmicutes 403175 93974 112370 57834
Fusobacteria 262 220 0 0
Gemmatimonadetes 0 0 0 0
Nitrospirae 0 0 0 0
Opisthokonta 0 0 0 0
Planctomycetes 0 0 0 0
Proteobacteria 38307 82818 12867 106564
Spirochaetes 88 0 0 0
Synergistetes 78 0 0 0
Tenericutes 217 0 0 0
Thermotogae 0 0 0 0
Unclassified Bacteria 37700 2264 22823 3352
Total reads 483929 179907 156550 189480
Bacteroidetes% 0.27566 0.24124 5.20281 11.3885
Firmicutes% 83.3128 52.2348 71.779 30.5225
Bacte+Firmi% 83.5885 52.476 76.9818 41.911
Bacte/Firmi% 0.33087 0.46183 7.24838 37.312
Proteo% 7.91583 46.0338 8.2191 56.2402
