Supplementary Table 2. Raw data from a 100% stacked bar chart showing microbiota analysis at the phylum level in 19 patients with UC before undergoing AFM therapy (a), after AFM therapy (b), at 4 weeks after AFM therapy (c) and at 8 weeks after AFM therapy (d).
UC patients at baseline
1a 2a 3a 4a 5a 6a 7a 8a 9a
Actinobacteria 1180 296 1076 433 478 1751 8252 1637 1985
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chloro bi
65389 51394 11756 17027 13698 12159 10889 61777 64968
Chlamydiae/Verruco microbia group
0 0 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 0 0 70 0 0 0 0 0 0
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus- Thermus
0 0 0 0 0 0 0 0 0
Fibrobacteres/Acidob acteria group
0 0 0 0 0 0 0 0 0
Firmicutes 193902 53843 109519 126502 198169 80492 154898 158014 204494
Fusobacteria 0 9677 0 4302 0 9147 0 0 0
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 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 71964 40619 23497 7934 42520 93880 73 96357 39811
Spirochaetes 74 0 0 0 0 0 0 0 0
Synergistetes 0 0 0 0 0 0 0 0 0
Tenericutes 0 0 0 0 0 51 0 0 0
Thermotogae 0 0 0 0 0 0 0 0 0
Unclassified Bacteria 46437 38133 13141 23416 18102 18870 30525 46142 34994 Total reads 378946 193962 159059 179614 272967 216350 204637 363927 346252 Bacteroidetes% 17.2554
9
26.4969 4
7.39096 8
9.47977 3
5.01818 9
5.62006 0
5.32112 9
16.9751 0
18.7632 1 Firmicutes% 51.1687 27.7595 68.8543 70.4299 72.5981 37.2045 75.6940 43.4191 59.0592
6 6 2 2 5 2 3 4 9 Bacte+Firmi% 68.4242
6
54.2565 0
76.2452 9
79.9096 9
77.6163 4
42.8245 8
81.0151 6
60.3942 5
77.8225 1 Bacte/Firmi% 33.7227
0
95.4515 9
10.7342 1
13.4598 6
6.91228 1
15.1058 4
7.02978 73
39.0959 02
31.7701 2
Proteo% 18.9905
6858
20.9417 3085
14.7725 058
4.41725 0326
15.5769 7451
43.3926 508
0.03567 2923
26.4770 1325
11.4976 9532
10a 11a 12a 13a 14a 15a 16a 17a 18a 19a
1857 12979 21218 393 2711 3403 7050 2443 530 2451
0 0 0 0 0 0 0 0 0 0
25398 50566 915 169 2384 1019 11959 20660 54867 983
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
205727 189142 304643 236313 119256 261368 126085 110097 122201 172277
0 135 0 14405 0 0 52 0 0 139
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
33564 13226 6577 105566 1079 3279 13953 2037 9666 6908
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
36078 47490 19222 22783 9436 12202 6979 12540 26850 2633
302624 313538 352575 379629 134866 281271 166078 147777 214114 185391
8.392592 788
16.12755 073
0.259519 251
0.044517 147
1.767680 513
0.362284 061
7.200833 343
13.98052 471
25.62513 427
0.530230 702 67.98105 60.32506 86.40516 62.24840 88.42554 92.92390 75.91914 74.50212 57.07286 92.92630
9 427 202 568 832 613 643 144 772 171 76.37365
179
76.45261 499
86.66468 127
62.29292 283
90.19322 883
93.28619 019
83.11997 977
88.48264 615
82.69800 2
93.45653 241 12.34548
69
26.73441 11
0.300351 55
0.071515 32
1.999060 8
0.389871 7
9.484871 3
18.76527 0
44.89897 7
0.570592 7 11.09099
08
4.218308 46
1.865418 70
27.80767 53
0.800053 3
1.165779 6
8.401474 0
1.378428 3
4.514417 5
3.726178 7
after AFM therapy 1b 2b 3b 4b 5b 6b 7b 8b 9b
Actinobacteria 176 219 1112 184 0 368 1041 1947 0
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chlor obi group
55 96 0 0 0 159 61 175 3092
Chlamydiae/Verruco microbia group
0 0 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 0 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 0 0 0
Fibrobacteres/Acido bacteria group
0 0 0 0 0 0 0 0 0
Firmicutes 83851 20812 139494 61125 757 238123 236562 247914 79165
Fusobacteria 0 0 0 0 0 0 0 0 0
Gemmatimonadete s
0 0 0 0 0 0 0 0 0
Nitrospirae 0 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 159595 75332 21390 69563 71750 68617 104722 136800 81722
Spirochaetes 108 0 0 0 0 0 0 0 0
Synergistetes 0 0 0 0 0 0 0 0 0
Tenericutes 0 0 0 0 0 0 0 0 0
Thermotogae 0 0 0 0 0 0 0 0 0 Unclassified
Bacteria
2664 1208 1181 3026 1012 4636 4519 4327 4664
Total reads 246449 97667 163177 133898 73519 311903 346905 391163 168643
Bacteroidetes% 0.02231 6
0.09829 3
0 0 0 0.05097
7
0.01758 4
0.04473 8
1.83345 8 Firmicutes% 34.0236
7224
21.3091 4229
85.4863 1241
45.6504 2047
1.02966 5801
76.3452 0989
68.1921 5635
63.3786 9379
46.9423 5752 Bacte+Firmi% 34.0459
89
21.4074 35
85.4863 12
45.6504 20
1.02966 58
76.3961 87
68.2097 40
63.4234 3
48.7758 1 Bacte/Firmi% 0.06559
2
0.46127 2
0 0 0 0.06677
2
0.02578 6
0.07058 8
3.90576 6
Proteo% 64.7578
20
77.1314 77
13.1084 6
51.9522 32
97.5938 19
21.9994 67
30.1875 15
34.9726 32
48.4585 7
10b 11b 12b 13b 14b 15b 16b 17b 18b 19b
923 703 102 3392 90 2147 237 57 4102 357
0 0 0 0 0 0 0 0 0 0
1154 570 123 546 475 1387 203 0 2489 4189
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
91305 103001 194707 157790 63832 199939 45818 56857 77229 143796
0 0 0 0 0 0 0 0 0 5461
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
123979 98387 4525 70723 32289 5790 15823 19253 28659 34711
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 470 0
0 0 0 0 0 0 0 0 0 0
10453 1648 5660 3795 895 585 1896 469 3719 50701
227814 204309 205117 236246 97581 209848 63977 76636 116668 239215
0.5065535 92
0.2789891 78
0.059965 776
0.2311150 24
0.486775 089
0.660954 596
0.317301 53
0 2.133404
19
1.751144 368 40.078748
45
50.414323 4
94.92484 777
66.790548 83
65.41437 37
95.27801 075
71.61636 213
74.19098 074
66.19552 919
60.11161 507 40.585302
04
50.693312 58
94.98481 355
67.021663 86
65.90114 879
95.93896 535
71.93366 366
74.19098 074
68.32893 338
61.86275 944 1.2638957
34
0.5533926 86
0.063171 843
0.3460295 33
0.744140 87
0.693711 582
0.443057 314
0 3.222882
596
2.913154 747 54.421150
59
48.155979 42
2.206058 006
29.936168 23
33.08943 339
2.759139 949
24.73232 568
25.12265 776
24.56457 64
14.51037 769
at 4 weeks after AFM 1c 2c 3c 4c 5c 6c 7c 8c 9c
Actinobacteria 2504 197 345 151 222 338 8262 402 143
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chloro bi group
1334 434 8145 21579 1226 0 0 173 235
Chlamydiae/Verruco microbia group
0 0 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 164 0 0 0 0 0 0 0 0
Deferribacteres 0 0 0 0 0 0 0 0 0
Deinococcus- Thermus
100 0 0 0 0 0 0 0 0
Fibrobacteres/Acidob acteria group
0 0 0 0 0 0 0 0 0
Firmicutes 403175 93974 112370 57834 155626 181356 281959 262147 13499
5
Fusobacteria 262 220 0 0 95 0 0 94 75
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 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 38307 82818 12867 106564 76986 6910 35298 25210 33427
Spirochaetes 88 0 0 0 0 0 0 0 0
Synergistetes 78 0 0 0 0 0 0 0 0
Tenericutes 217 0 0 0 0 0 0 0 0
Thermotogae 0 0 0 0 0 0 0 0 0
Unclassified Bacteria
37700 2264 22823 3352 27316 40911 9939 60646 27574
Total reads 483929 179907 156550 189480 261471 229515 335458 348672 19644
9 Bacteroidetes% 0.275660
272
0.24123 575
5.202810 604
11.38853 705
0.468885 651
0 0 0.049616
832
0.1196 23923 Firmicutes% 83.31284
1
52.2347 65
71.77898 4
30.52248 2
59.51941 1
79.0170 57
84.0519 52
75.18441 4
68.717 58 Bacte+Firmi% 83.58850 52.4760
0
76.98179 41.91101 59.98829 79.0170 5
84.0519 5
75.23403 68.837 20 Bacte/Firmi% 0.330873 0.46182
9
7.248375 37.31196 0.787786 0 0 0.065993 0.1740
8
Proteo% 7.915830
6
46.0337 8
8.219099 3
56.24023 6
29.44341 8
3.01069 6
10.5223 3
7.230290 9
17.015 6
10c 11c 12c 13c 14c 15c 16c 17c 18c 19c
3018 271 8080 188 2096 1270 439 254 380 131
0 0 0 0 0 0 0 0 0 0
467 85 51386 0 21708 262 202 28061 1461 103
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
448487 35351 177265 63310 142948 162357 94762 80915 37040 106856
0 0 174 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
35309 97 5863 20988 5642 6034 31145 16749 18330 92764
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
11222 13205 26477 1319 9267 8809 6042 4428 2405 3021
498503 49009 269245 85805 181661 178732 132590 130407 59616 202875
0.0936804 79
0.1734375 32
19.08521 978
0 11.94973
054
0.146588 188
0.152349 348
21.51801 667
2.450684 38
0.0507701 79 89.966760
48
72.131649 29
65.83780 572
73.78357 905
78.68942 701
90.83823 826
71.46994 494
62.04804 957
62.13097 155
52.670856 44 90.060440
96
72.305086 82
84.92302 55
73.78357 905
90.63915 755
90.98482 644
71.62229 429
83.56606 624
64.58165 593
52.721626 62 0.1041278
79
0.2404458 15
28.98823 795
0 15.18594
174
0.161372 777
0.213165 615
34.67960 205
3.944384 449
0.0963914 05 7.0830065
2
0.1979228 2.177570 61
24.46011 30
3.105784 95
3.376004 2
23.48970 5
12.84363 5
30.74677 9
45.724707
at 8 weeks after AFM 1d 2d 3d 4d 5d 6d 7d 8d 9d
Actinobacteria 3455 2863 643 165 1038 769 353 2181 305
Aquificae 0 0 0 0 0 0 0 0 0
Bacteroidetes/Chloro bi group
33941 165 8400 0 2345 8079 73 54 41912
Chlamydiae/Verruco microbia group
0 0 0 0 0 0 0 0 0
Chloroflexi 0 0 0 0 0 0 0 0 0
Chrysiogenetes 0 0 0 0 0 0 0 0 0
Cyanobacteria 0 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 0 0 0
Fibrobacteres/Acidob 0 0 0 0 0 0 0 0 0
acteria group
Firmicutes 374125 108243 128486 82398 141006 96995 305622 282432 115361
Fusobacteria 0 0 0 0 0 0 0 0 0
Gemmatimonadetes 0 0 0 0 0 0 0 0 0
Nitrospirae 0 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 14438 17611 28046 47857 5177 81430 1453 6708 39874
Spirochaetes 63 0 0 0 0 0 0 0 0
Synergistetes 0 0 0 0 0 0 0 0 0
Tenericutes 83 0 0 0 0 0 0 0 0
Thermotogae 0 0 0 0 0 0 0 0 0
Unclassified Bacteria
47962 13511 35487 5575 30234 18171 34839 44343 35519
Total reads 474067 142393 201062 135995 179800 205444 342340 335718 232971 Bacteroidetes% 7.15953
6521
0.115876 483
4.177815 798
0 1.304226
919
3.932458 48
0.02132 383
0.016084 928
17.9902 2196 Firmicutes% 78.9181
6979
76.01707 949
63.90367 15
60.5889 9224
78.42380 423
47.21237 904
89.2744 0556
84.12775 008
49.5173 219 Bacte+Firmi% 86.0777
0632
76.13295 597
68.08148 73
60.5889 9224
79.72803 115
51.14483 752
89.2957 2939
84.14383 5
67.5075 4386 Bacte/Firmi% 9.07210
1
0.152434 6.537677 0 1.663049 8.329295 0.02388 5
0.019119 36.3311 6
Proteo% 3.04556
1
12.36788 13.94893 35.1902 6
2.879310 39.63610 0.42443 1
1.998105 17.1154 3
10d 11d 12d 13d 14d 15d 16d
2080 1446 22008 300 1685 1433 199
0 0 0 0 0 0 0
248 46140 2270 0 26745 71 104
0 586 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
391254 297332 505487 209312 120334 138120 124455
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
3154 17163 13843 60090 62048 3944 34088
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
36909 41172 50461 9617 19682 7915 16668
433645 403839 594069 279319 230494 151483 175514
0.057189637 11.42534525 0.382110496 0 11.60333892 0.046869946 0.059254532 90.22449238 73.62637091 85.08893748 74.93654209 52.20699888 91.17854809 70.90887337 90.28168202 85.05171615 85.47104798 74.93654209 63.8103378 91.22541803 70.9681279 0.063385933 15.51800681 0.449071885 0 22.22563864 0.051404576 0.083564341 0.727323041 4.249960999 2.330200701 21.51303707 26.91957274 2.603592482 19.4218125
