Pull Information from Phyloseq Object
pullSampleAbundance(x, ...)
pullTaxaAbundance(x, ...)
pullTaxaRank(x, ...)phyloseq object
Option to pass on to pull. Only when using
filterSampleData or filterTaxaData
sample data or taxonomy table as tibble.
A vector of requested value
These are alternative to subset and prune functions in
phyloseq.
The pullSampleAbundance can be used to get abundances of all taxa.
The pullTaxaAbundance can be used to get abundances of a taxa in all
samples.
The pullSampleVariable can be used to get all variables within a
column in sample_data.
The pullTaxaRank can be used to get all taxomic information at a
particular rank in tax_table.
The naming is using pull because it uses the dplyr::pull function.
Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils
library(biomeUtils)
data("FuentesIliGutData")
pullSampleAbundance(FuentesIliGutData, "sample_1", name= "FeatureID")
#> ASV302 ASV636 ASV500 ASV7 ASV2617 ASV148 ASV196 ASV2699 ASV109 ASV1472
#> 8 0 0 818 0 7 17 0 0 0
#> ASV697 ASV1357 ASV746 ASV309 ASV2668 ASV2467 ASV2819 ASV557 ASV1657 ASV397
#> 1 0 0 0 0 0 0 0 0 21
#> ASV97 ASV1271 ASV589 ASV644 ASV1623 ASV15 ASV1123 ASV186 ASV716 ASV337
#> 123 0 0 2 0 301 3 0 0 12
#> ASV2028 ASV1899 ASV1438 ASV691 ASV1772 ASV1726 ASV381 ASV807 ASV1639 ASV3242
#> 0 0 0 0 6 1 0 0 0 0
#> ASV1337 ASV562 ASV1860 ASV249 ASV24 ASV971 ASV879 ASV240 ASV992 ASV1660
#> 0 1 0 0 179 0 0 0 0 2
#> ASV840 ASV152 ASV1480 ASV798 ASV285 ASV720 ASV1266 ASV768 ASV57 ASV2623
#> 0 5 0 0 0 2 0 0 63 0
#> ASV1998 ASV251 ASV3060 ASV96 ASV577 ASV2020 ASV1602 ASV2830 ASV165 ASV1088
#> 0 0 0 3 6 0 0 0 0 0
#> ASV5 ASV18 ASV585 ASV296 ASV1085 ASV20 ASV1555 ASV1154 ASV2309 ASV3174
#> 630 369 0 0 2 130 0 0 0 0
#> ASV795 ASV1521 ASV1022 ASV351 ASV1668 ASV292 ASV2544 ASV414 ASV273 ASV2120
#> 0 0 0 0 0 0 0 0 12 0
#> ASV2022 ASV2561 ASV83 ASV561 ASV307 ASV774 ASV1143 ASV2578 ASV2031 ASV286
#> 1 0 23 22 0 0 0 0 0 7
#> ASV1259 ASV1839 ASV193 ASV112 ASV380 ASV538 ASV491 ASV157 ASV266 ASV525
#> 1 0 0 0 0 0 0 12 0 0
#> ASV25 ASV1937 ASV323 ASV26 ASV893 ASV760 ASV717 ASV14 ASV72 ASV279
#> 22 0 0 0 0 0 0 219 0 0
#> ASV570 ASV1786 ASV287 ASV844 ASV174 ASV1710 ASV1493 ASV1704 ASV728 ASV10
#> 0 0 8 0 21 0 0 0 0 32
#> ASV282 ASV60 ASV163 ASV56 ASV120 ASV108 ASV770 ASV2601 ASV2449 ASV1778
#> 0 2 39 0 10 15 8 0 0 0
#> ASV415 ASV1221 ASV1307 ASV1585 ASV168 ASV2729 ASV607 ASV646 ASV1777 ASV427
#> 0 0 0 0 0 0 0 0 0 0
#> ASV1210 ASV1837 ASV1684 ASV260 ASV1752 ASV2421 ASV99 ASV235 ASV67 ASV350
#> 0 0 0 0 0 0 8 0 48 6
#> ASV75 ASV2432 ASV1228 ASV263 ASV95 ASV79 ASV781 ASV1817 ASV1631 ASV1315
#> 0 0 0 7 60 0 0 0 0 0
#> ASV76 ASV453 ASV2321 ASV825 ASV2024 ASV1524 ASV827 ASV709 ASV34 ASV1064
#> 0 9 2 0 0 0 0 0 42 0
#> ASV2006 ASV522 ASV1723 ASV2725 ASV874 ASV136 ASV754 ASV1581 ASV89 ASV1655
#> 0 0 0 0 0 4 0 0 59 0
#> ASV140 ASV599 ASV580 ASV949 ASV945 ASV132 ASV1646 ASV980 ASV356 ASV776
#> 20 0 0 17 0 0 0 2 0 0
#> ASV430 ASV400 ASV377 ASV657 ASV183 ASV1345 ASV2612 ASV550 ASV87 ASV2209
#> 0 0 0 0 0 0 0 4 0 0
#> ASV124 ASV160 ASV2537 ASV129 ASV1765 ASV295 ASV1099 ASV393 ASV1805 ASV861
#> 0 8 0 25 0 5 0 0 0 0
#> ASV406 ASV71 ASV250 ASV1332 ASV1966 ASV3573 ASV686 ASV1044 ASV1997 ASV364
#> 0 17 14 0 0 0 0 0 0 1
#> ASV1274 ASV766 ASV1009 ASV1214 ASV718 ASV2372 ASV73 ASV563 ASV1297 ASV857
#> 0 0 0 0 0 2 13 0 0 0
#> ASV1265 ASV54 ASV586 ASV1476 ASV913 ASV519 ASV1107 ASV1479 ASV2772 ASV850
#> 0 0 4 0 7 0 0 0 0 0
#> ASV2480 ASV1554 ASV176 ASV396 ASV2730 ASV113 ASV693 ASV212 ASV383 ASV228
#> 0 0 6 0 0 47 0 0 0 5
#> ASV207 ASV851 ASV2558 ASV194 ASV142 ASV81 ASV343 ASV1111 ASV558 ASV537
#> 64 0 0 3 0 37 0 6 0 0
#> ASV615 ASV785 ASV1430 ASV1700 ASV4203 ASV166 ASV379 ASV294 ASV526 ASV433
#> 0 2 0 0 0 6 0 0 0 2
#> ASV359 ASV805 ASV2190 ASV1225 ASV511 ASV510 ASV214 ASV569 ASV541 ASV579
#> 0 2 0 0 0 0 0 0 0 0
#> ASV932 ASV1656 ASV654 ASV137 ASV116 ASV1658 ASV50 ASV735 ASV608 ASV1923
#> 0 0 0 0 0 0 206 0 0 0
#> ASV325 ASV85 ASV36 ASV339 ASV47 ASV150 ASV22 ASV338 ASV204 ASV1206
#> 7 313 283 3 11 0 281 0 2 0
#> ASV1068 ASV2454 ASV4 ASV147 ASV2105 ASV342 ASV407 ASV3610 ASV658 ASV477
#> 0 0 522 23 0 0 0 0 0 0
#> ASV2025 ASV329 ASV46 ASV560 ASV224 ASV88 ASV703 ASV1619 ASV1831 ASV405
#> 0 3 109 0 16 35 6 0 0 0
#> ASV131 ASV673 ASV626 ASV334 ASV326 ASV1663 ASV2263 ASV1742 ASV1124 ASV3578
#> 0 5 0 0 0 6 0 0 0 0
#> ASV93 ASV451 ASV3241 ASV52 ASV2858 ASV51 ASV1690 ASV1012 ASV513 ASV1002
#> 0 0 0 137 0 47 2 0 0 2
#> ASV162 ASV954 ASV159 ASV8 ASV892 ASV846 ASV290 ASV1201 ASV1401 ASV1101
#> 15 3 7 105 0 8 4 0 0 0
#> ASV267 ASV552 ASV2157 ASV613 ASV1207 ASV528 ASV540 ASV1016 ASV2126 ASV575
#> 0 0 0 0 0 0 0 0 0 0
#> ASV1084 ASV539 ASV1041 ASV1681 ASV252 ASV1748 ASV376 ASV39 ASV391 ASV305
#> 0 0 0 0 2 0 26 0 0 0
#> ASV740 ASV1328 ASV565 ASV173 ASV1244 ASV62 ASV1683 ASV2483 ASV1186 ASV80
#> 0 0 0 0 2 2 0 0 0 0
#> ASV617 ASV146 ASV114 ASV2106 ASV492 ASV466 ASV694 ASV181 ASV434 ASV958
#> 13 61 0 0 2 0 0 0 0 0
#> ASV2081 ASV169 ASV548 ASV1992 ASV40 ASV1007 ASV641 ASV368 ASV106 ASV2637
#> 0 0 2 0 78 0 0 0 0 0
#> ASV679 ASV475 ASV677 ASV78 ASV390 ASV630 ASV270 ASV394 ASV1445 ASV238
#> 0 0 0 0 0 0 6 0 0 0
#> ASV65 ASV1442 ASV930 ASV2166 ASV6 ASV684 ASV184 ASV952 ASV135 ASV474
#> 87 0 0 0 1174 0 17 0 11 0
#> ASV1711 ASV758 ASV1448 ASV2064 ASV322 ASV199 ASV1150 ASV1269 ASV1676 ASV480
#> 0 0 0 0 0 0 0 0 0 1
#> ASV2066 ASV530 ASV463 ASV110 ASV289 ASV42 ASV1404 ASV217 ASV1604 ASV464
#> 0 0 0 0 0 39 0 6 0 0
#> ASV2242 ASV3545 ASV672 ASV98 ASV736 ASV90 ASV2041 ASV454 ASV1434 ASV3397
#> 0 0 3 1 0 0 0 0 0 0
#> ASV1267 ASV1580 ASV509 ASV243 ASV115 ASV2036 ASV1272 ASV763 ASV1050 ASV1929
#> 1 2 47 0 0 0 0 0 0 0
#> ASV1670 ASV1890 ASV1953 ASV190 ASV382 ASV17 ASV219 ASV1935 ASV185 ASV205
#> 0 0 0 0 0 253 8 0 0 104
#> ASV1991 ASV1956 ASV420 ASV849 ASV886 ASV2051 ASV370 ASV1603 ASV213 ASV117
#> 0 0 3 0 0 0 0 0 0 48
#> ASV2852 ASV411 ASV2804 ASV1659 ASV1066 ASV487 ASV261 ASV793 ASV664 ASV847
#> 0 16 0 0 0 0 12 0 3 2
#> ASV1026 ASV233 ASV692 ASV3840 ASV1 ASV291 ASV1030 ASV2030 ASV1633 ASV74
#> 0 0 0 0 734 18 1 3 0 25
#> ASV304 ASV347 ASV37 ASV330 ASV639 ASV609 ASV576 ASV1397 ASV425 ASV705
#> 0 0 33 0 0 15 2 0 0 0
#> ASV484 ASV1936 ASV268 ASV734 ASV107 ASV70 ASV918 ASV49 ASV195 ASV230
#> 0 0 0 0 71 0 0 108 0 0
#> ASV1648 ASV1680 ASV284 ASV2718 ASV187 ASV231 ASV177 ASV1853 ASV201 ASV385
#> 0 2 0 0 0 0 0 0 0 0
#> ASV2004 ASV860 ASV521 ASV2814 ASV1527 ASV41 ASV2310 ASV700 ASV737 ASV683
#> 0 0 0 0 3 0 0 0 0 9
#> ASV1468 ASV2226 ASV2697 ASV597 ASV1053 ASV441 ASV1008 ASV890 ASV496 ASV324
#> 3 0 0 0 0 0 0 0 0 2
#> ASV2353 ASV255 ASV21 ASV247 ASV2325 ASV254 ASV948 ASV2265 ASV621 ASV924
#> 0 0 991 1 0 0 0 0 0 0
#> ASV3251 ASV2383 ASV128 ASV489 ASV602 ASV2415 ASV545 ASV867 ASV2018 ASV100
#> 0 0 0 0 0 0 0 0 1 0
#> ASV1263 ASV2733 ASV19 ASV978 ASV94 ASV167 ASV12 ASV573 ASV1727 ASV104
#> 3 0 0 1 13 84 431 0 0 0
#> ASV944 ASV1627 ASV308 ASV1103 ASV69 ASV1421 ASV1023 ASV862 ASV2035 ASV1586
#> 0 0 0 0 149 0 0 0 0 0
#> ASV429 ASV756 ASV111 ASV469 ASV1360 ASV961 ASV1902 ASV333 ASV209 ASV493
#> 0 0 86 0 0 1 0 2 0 0
#> ASV1638 ASV719 ASV534 ASV413 ASV155 ASV708 ASV1732 ASV30 ASV409 ASV179
#> 0 0 4 18 0 0 0 30 0 0
#> ASV1128 ASV27 ASV870 ASV3324 ASV9 ASV45 ASV1330 ASV907 ASV1536 ASV920
#> 3 0 0 0 0 0 0 0 0 15
#> ASV216 ASV32 ASV1319 ASV3127 ASV787 ASV375 ASV623 ASV2610 ASV61 ASV587
#> 0 150 0 0 50 0 0 0 3 0
#> ASV31 ASV1492 ASV1173 ASV2557 ASV995 ASV2870 ASV858 ASV392 ASV316 ASV448
#> 23 0 0 1 0 0 0 8 3 0
#> ASV153 ASV421 ASV281 ASV1451 ASV3411 ASV11 ASV245 ASV101 ASV16 ASV1305
#> 0 9 0 0 0 5 0 38 70 0
#> ASV926 ASV2324 ASV428 ASV2013 ASV796 ASV2247 ASV2425 ASV2404 ASV203 ASV102
#> 0 0 0 0 0 0 0 0 0 0
#> ASV1363 ASV58 ASV1130 ASV141 ASV452 ASV2786 ASV423 ASV1885 ASV180 ASV416
#> 0 0 0 2 0 0 1 0 0 0
#> ASV1530 ASV225 ASV483 ASV1226 ASV934 ASV2188 ASV226 ASV336 ASV801 ASV2075
#> 0 7 0 0 0 0 0 0 0 0
#> ASV2849 ASV1340 ASV353 ASV1503 ASV1076 ASV218 ASV3181 ASV2473 ASV2327 ASV387
#> 0 3 0 0 0 0 0 0 0 0
#> ASV887 ASV592 ASV64 ASV2455 ASV242 ASV91 ASV2742 ASV817 ASV1616 ASV546
#> 0 19 0 0 6 1 0 15 0 0
#> ASV189 ASV982 ASV84 ASV1628 ASV341 ASV200 ASV645 ASV803 ASV517 ASV154
#> 43 0 104 0 14 8 6 0 0 0
#> ASV232 ASV1234 ASV1017 ASV229 ASV1714 ASV1358 ASV1809 ASV161 ASV1823 ASV553
#> 4 0 0 7 0 0 0 37 0 0
#> ASV1097 ASV631 ASV2 ASV133 ASV567 ASV593 ASV119 ASV125 ASV1129 ASV275
#> 0 5 302 73 14 0 6 46 0 12
#> ASV1596 ASV197 ASV221 ASV361 ASV1761 ASV701 ASV707 ASV1701 ASV843 ASV1820
#> 0 0 25 6 0 0 0 0 0 0
#> ASV44 ASV126 ASV23 ASV130 ASV13 ASV880 ASV3076 ASV48 ASV859 ASV1109
#> 127 5 13 73 90 0 1 69 0 0
#> ASV53 ASV2298 ASV1372 ASV578 ASV328 ASV118 ASV1850 ASV2752 ASV1209 ASV237
#> 93 1 0 10 0 82 0 0 1 0
#> ASV1056 ASV3002 ASV543 ASV1949 ASV211 ASV986 ASV1484 ASV366 ASV422 ASV272
#> 0 0 0 0 0 0 0 2 0 0
#> ASV1125 ASV1855 ASV2985 ASV1398 ASV149 ASV399 ASV794 ASV55 ASV527 ASV33
#> 0 0 0 0 0 5 0 62 0 173
#> ASV63 ASV2277 ASV355 ASV642 ASV502 ASV239 ASV542 ASV911 ASV66 ASV1889
#> 49 0 7 2 0 14 0 0 1 2
#> ASV472 ASV156 ASV702 ASV1452 ASV77 ASV404 ASV797 ASV403 ASV468 ASV660
#> 0 13 0 0 34 21 0 0 0 0
#> ASV2079 ASV1246 ASV363 ASV257 ASV1630 ASV2878 ASV151 ASV92 ASV762 ASV1614
#> 1 0 0 0 2 0 0 10 3 0
#> ASV832 ASV68 ASV2809 ASV1905 ASV1642 ASV227 ASV590 ASV178 ASV544 ASV933
#> 0 0 0 0 0 11 0 0 0 2
#> ASV1086 ASV504 ASV445 ASV638 ASV1516 ASV1487 ASV82 ASV410 ASV2332 ASV771
#> 0 0 0 2 0 0 1 1 0 29
#> ASV1682 ASV2322 ASV349 ASV262 ASV559 ASV1096 ASV898 ASV144 ASV35 ASV1077
#> 0 0 0 0 0 0 1 10 1190 0
#> ASV139 ASV143 ASV1148 ASV1613 ASV2462 ASV301 ASV671 ASV1218 ASV43 ASV444
#> 29 35 0 0 0 4 0 0 87 0
#> ASV1163 ASV105 ASV384 ASV485 ASV2486 ASV739 ASV369 ASV164 ASV3 ASV1079
#> 0 0 44 0 0 0 0 0 479 0
#> ASV810 ASV145 ASV288 ASV594 ASV2503 ASV258 ASV1974 ASV3490 ASV311 ASV29
#> 0 0 0 0 0 0 1 0 0 199
#> ASV274 ASV1589 ASV783 ASV711 ASV170 ASV591 ASV497 ASV442 ASV1707 ASV1915
#> 0 0 3 0 17 0 18 1 0 0
#> ASV1812 ASV182 ASV1115 ASV1878 ASV297 ASV38 ASV652 ASV59 ASV103 ASV582
#> 5 9 0 0 99 62 0 12 0 0
#> ASV724 ASV28 ASV2286 ASV253 ASV443
#> 0 0 0 9 0
pullTaxaAbundance(FuentesIliGutData, "ASV1", name = "SampleID")
#> sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 sample_7
#> 734 1587 289 401 422 361 508
#> sample_8 sample_9 sample_10 sample_11 sample_12 sample_13 sample_14
#> 940 2060 427 235 231 377 422
#> sample_15 sample_16 sample_17 sample_18 sample_19 sample_20 sample_21
#> 70 1155 1023 712 435 2131 1143
#> sample_22 sample_23 sample_24 sample_25 sample_26 sample_27 sample_28
#> 308 2718 625 867 288 105 204
#> sample_29 sample_30 sample_31 sample_32 sample_33 sample_34 sample_35
#> 508 1054 586 1576 1815 1434 537
#> sample_36 sample_37 sample_38 sample_39 sample_40 sample_41 sample_42
#> 7719 7151 1356 1471 1197 459 806
#> sample_43 sample_44 sample_45 sample_46 sample_47 sample_48 sample_49
#> 6077 2737 804 795 532 559 974
#> sample_50 sample_51 sample_52 sample_53 sample_54 sample_55 sample_56
#> 3449 893 1625 1010 169 203 494
#> sample_57 sample_58 sample_59 sample_60 sample_61 sample_62 sample_63
#> 3435 829 490 134 286 543 886
#> sample_64 sample_65 sample_66 sample_67 sample_68 sample_69 sample_70
#> 973 727 62 1082 2762 269 734
#> sample_71 sample_72 sample_73 sample_74 sample_75 sample_76 sample_77
#> 61 994 173 560 226 73 43
#> sample_78 sample_79 sample_80 sample_81 sample_82 sample_83 sample_84
#> 367 82 736 379 90 256 6
#> sample_85 sample_86 sample_87 sample_88 sample_89 sample_90 sample_91
#> 944 263 719 100 82 973 1633
#> sample_92 sample_93 sample_94 sample_95 sample_96 sample_97 sample_98
#> 208 1665 345 517 5272 418 230
#> sample_99 sample_100 sample_101 sample_102 sample_103 sample_104 sample_105
#> 459 225 552 662 1728 607 1118
#> sample_106 sample_107 sample_108 sample_109 sample_110 sample_111 sample_112
#> 214 2731 1194 1147 477 488 122
#> sample_113 sample_114 sample_115 sample_116 sample_117 sample_118 sample_119
#> 785 476 321 798 1403 1316 2665
#> sample_120 sample_121 sample_122 sample_123 sample_124 sample_125 sample_126
#> 4253 280 1732 809 453 1016 2140
#> sample_127 sample_128 sample_129 sample_130 sample_131 sample_132 sample_133
#> 3836 516 249 739 11155 3469 2459
#> sample_134 sample_135 sample_136 sample_137 sample_138 sample_139 sample_140
#> 4529 997 4053 1485 730 831 6498
#> sample_141 sample_142 sample_143 sample_144 sample_145 sample_146 sample_147
#> 3174 2113 1117 1467 778 909 1750
#> sample_148 sample_149 sample_150 sample_151 sample_152 sample_153 sample_154
#> 2768 1042 4989 420 10504 207 62
#> sample_155 sample_156 sample_157 sample_158 sample_159 sample_160 sample_161
#> 436 992 3136 2763 967 238 2042
#> sample_162 sample_163 sample_164 sample_165 sample_166 sample_167 sample_168
#> 4500 1550 4691 3811 878 3226 1350
#> sample_169 sample_170 sample_171 sample_172 sample_173 sample_174 sample_175
#> 1199 3038 2058 3238 3762 837 581
#> sample_176 sample_177 sample_178 sample_179 sample_180 sample_181 sample_182
#> 1116 913 5836 1861 250 118 428
#> sample_183 sample_184 sample_185 sample_186 sample_187 sample_188 sample_189
#> 95 2150 185 3074 104 1107 6506
#> sample_190 sample_191 sample_192 sample_193 sample_194 sample_195 sample_196
#> 455 2766 206 212 8539 876 1012
#> sample_197 sample_198 sample_199 sample_200 sample_201 sample_202 sample_203
#> 106 1361 315 578 928 724 643
#> sample_204 sample_205 sample_206 sample_207 sample_208 sample_209 sample_210
#> 565 313 93 120 431 1951 102
#> sample_211 sample_212 sample_213 sample_214 sample_215 sample_216 sample_217
#> 59 4175 998 219 4138 354 95
#> sample_218 sample_219 sample_220 sample_221 sample_222 sample_223 sample_224
#> 566 186 193 396 126 1496 963
#> sample_225 sample_226 sample_227 sample_228 sample_229 sample_230 sample_231
#> 286 340 2830 6428 4249 1531 416
#> sample_232 sample_233 sample_234 sample_235 sample_236 sample_237 sample_238
#> 3056 3898 16181 461 3030 697 2096
#> sample_239 sample_240 sample_241 sample_242 sample_243 sample_244 sample_245
#> 6773 681 2680 6823 681 9937 1231
#> sample_246 sample_247 sample_248 sample_249 sample_250 sample_251 sample_252
#> 155 5203 453 2951 1626 3032 359
#> sample_253 sample_254 sample_255 sample_256 sample_257 sample_258 sample_259
#> 453 300 1191 1048 1469 1046 455
#> sample_260 sample_261 sample_262 sample_263 sample_264 sample_265 sample_266
#> 292 2589 4304 1022 1635 2339 558
#> sample_267 sample_268 sample_269 sample_270 sample_271 sample_272 sample_273
#> 517 1690 9145 2071 911 410 3519
#> sample_274 sample_275 sample_276 sample_277 sample_278 sample_279 sample_280
#> 6007 3362 701 3044 7306 1955 609
#> sample_281 sample_282 sample_283 sample_284 sample_285 sample_286 sample_287
#> 1831 1098 2439 27 960 407 12745
#> sample_288 sample_289 sample_290 sample_291 sample_292 sample_293 sample_294
#> 8159 909 8240 1465 1853 169 8866
#> sample_295 sample_296 sample_297 sample_298 sample_299 sample_300 sample_301
#> 6284 1446 2375 840 2087 6486 1747
#> sample_302 sample_303 sample_304 sample_305 sample_306 sample_307 sample_308
#> 562 524 1744 2205 6296 138 7474
#> sample_309 sample_310 sample_311 sample_312 sample_313 sample_314 sample_315
#> 3446 74 599 441 1384 31 642
#> sample_316 sample_317 sample_318 sample_319 sample_320 sample_321 sample_322
#> 702 311 186 2430 339 2981 897
#> sample_323 sample_324 sample_325 sample_326 sample_327 sample_328 sample_329
#> 335 415 1654 579 124 381 1529
#> sample_330 sample_331 sample_332 sample_333 sample_334 sample_335 sample_336
#> 2719 1119 162 1951 309 13 2227
#> sample_337 sample_338 sample_339 sample_340 sample_341 sample_342 sample_343
#> 1414 163 1055 161 706 1040 321
#> sample_344 sample_345 sample_346 sample_347 sample_348 sample_349 sample_350
#> 739 319 1388 999 651 1981 1267
#> sample_351 sample_352 sample_353 sample_354 sample_355 sample_356 sample_357
#> 862 3343 4104 794 5452 751 2404
#> sample_358 sample_359 sample_360 sample_361 sample_362 sample_363 sample_364
#> 505 8280 1130 958 5332 605 3931
#> sample_365 sample_366 sample_367 sample_368 sample_369 sample_370 sample_371
#> 376 1756 7317 1216 3809 1881 865
#> sample_372 sample_373 sample_374 sample_375 sample_376 sample_377 sample_378
#> 4796 340 120 2946 291 1363 781
#> sample_379 sample_380 sample_381 sample_382 sample_383 sample_384 sample_385
#> 301 2598 926 43 570 34 333
#> sample_386 sample_387 sample_388 sample_389 sample_390 sample_391 sample_392
#> 1950 1398 23 265 359 1540 556
#> sample_393 sample_394 sample_395 sample_396 sample_397 sample_398 sample_399
#> 179 495 2105 467 52 893 3999
#> sample_400 sample_401 sample_402 sample_403 sample_404 sample_405 sample_406
#> 3960 905 8908 4242 2094 565 2114
#> sample_407 sample_408 sample_409 sample_410 sample_411 sample_412 sample_413
#> 1756 5598 1180 9052 2333 8640 5427
#> sample_414 sample_415 sample_416 sample_417 sample_418 sample_419 sample_420
#> 2163 5166 2193 359 11837 2437 6347
#> sample_421 sample_422 sample_423 sample_424 sample_425 sample_426 sample_427
#> 2056 3023 20550 2576 1617 897 3519
#> sample_428 sample_429 sample_430 sample_431 sample_432 sample_433 sample_434
#> 785 1047 2739 2293 7350 5516 2676
#> sample_435 sample_436 sample_437 sample_438 sample_439 sample_440 sample_441
#> 774 3509 2914 12301 12679 1485 502
#> sample_442 sample_443 sample_444 sample_445 sample_446 sample_447 sample_448
#> 61 889 3436 2569 3631 3709 634
#> sample_449 sample_450 sample_451 sample_452 sample_453 sample_454 sample_455
#> 3012 5491 2964 2308 1045 941 3801
#> sample_456 sample_457 sample_458 sample_459 sample_460 sample_461 sample_462
#> 2089 2237 2378 16952 3783 8642 2835
#> sample_463 sample_464 sample_465 sample_466 sample_467 sample_468 sample_469
#> 3249 1900 2734 4679 5633 6142 7652
#> sample_470 sample_471 sample_472 sample_473 sample_474 sample_475 sample_476
#> 9111 2134 9 964 2268 1689 1559
#> sample_477 sample_478 sample_479 sample_480 sample_481 sample_482 sample_483
#> 869 3635 1316 1207 1648 1365 2300
#> sample_484 sample_485 sample_486 sample_487 sample_488 sample_489 sample_490
#> 1287 1237 6730 719 14163 5394 594
#> sample_491 sample_492 sample_493 sample_494 sample_495 sample_496 sample_497
#> 7765 281 5436 711 665 5216 381
#> sample_498 sample_499 sample_500 sample_501 sample_502 sample_503 sample_504
#> 459 6864 995 2280 543 828 549
#> sample_505 sample_506 sample_507 sample_508 sample_509 sample_510 sample_511
#> 2452 13856 1583 110 69 773 1476
#> sample_512 sample_513 sample_514 sample_515 sample_516 sample_517 sample_518
#> 4822 1055 6109 52 1714 2617 474
#> sample_519 sample_520 sample_521 sample_522 sample_523 sample_524 sample_525
#> 1380 455 11791 1559 722 3618 10102
#> sample_526 sample_527 sample_528 sample_529 sample_530 sample_531 sample_532
#> 356 1263 21737 1765 1500 6284 3242
#> sample_533 sample_534 sample_535 sample_536 sample_537 sample_538 sample_539
#> 1839 11847 3477 2532 1005 1011 3143
#> sample_540 sample_541 sample_542 sample_543 sample_544 sample_545 sample_546
#> 5819 143 1782 1703 4649 1054 1675
#> sample_547 sample_548 sample_549 sample_550 sample_551 sample_552 sample_553
#> 729 4559 2695 3379 839 1606 5523
#> sample_554 sample_555 sample_556 sample_557 sample_558 sample_559 sample_560
#> 1150 863 918 20718 788 311 2321
#> sample_561 sample_562 sample_563 sample_564 sample_565 sample_566 sample_567
#> 306 1013 1691 221 14837 5114 1348
#> sample_568 sample_569 sample_570 sample_571 sample_572 sample_573 sample_574
#> 1577 123 16 464 2495 1861 3037
#> sample_575 sample_576 sample_577 sample_578 sample_579 sample_580 sample_581
#> 1567 704 1342 1480 626 4762 516
#> sample_582 sample_583 sample_584 sample_585 sample_586 sample_587 sample_588
#> 6057 5787 5689 4388 3065 1687 1128
#> sample_589
#> 7011
pullTaxaRank(FuentesIliGutData, "Genus")
#> [1] "Lachnospiraceae NC2004 group"
#> [2] "Ruminococcaceae UCG-013"
#> [3] NA
#> [4] "Fusicatenibacter"
#> [5] NA
#> [6] NA
#> [7] "Roseburia"
#> [8] "Butyricicoccus"
#> [9] "Alistipes"
#> [10] "Oscillibacter"
#> [11] NA
#> [12] NA
#> [13] "Ruminococcaceae UCG-013"
#> [14] "[Eubacterium] coprostanoligenes group"
#> [15] NA
#> [16] "Lachnospiraceae FE2018 group"
#> [17] "Ruminococcaceae NK4A214 group"
#> [18] "Family XIII AD3011 group"
#> [19] NA
#> [20] "Christensenellaceae R-7 group"
#> [21] "Coprococcus 2"
#> [22] NA
#> [23] NA
#> [24] "Ruminiclostridium"
#> [25] NA
#> [26] "Anaerostipes"
#> [27] "Lachnospiraceae FCS020 group"
#> [28] "Ruminococcaceae UCG-014"
#> [29] NA
#> [30] "Ruminiclostridium 5"
#> [31] "Actinomyces"
#> [32] "Dielma"
#> [33] "Blautia"
#> [34] "Clostridium sensu stricto 1"
#> [35] NA
#> [36] "Pseudomonas"
#> [37] NA
#> [38] "Bifidobacterium"
#> [39] "Family XIII AD3011 group"
#> [40] NA
#> [41] "Erysipelatoclostridium"
#> [42] "Oscillibacter"
#> [43] "Gemella"
#> [44] "Sutterella"
#> [45] "Bifidobacterium"
#> [46] "Coprobacter"
#> [47] "GCA-900066575"
#> [48] "Bilophila"
#> [49] "Eggerthella"
#> [50] NA
#> [51] "Peptococcus"
#> [52] "Bacteroides"
#> [53] NA
#> [54] NA
#> [55] "[Eubacterium] coprostanoligenes group"
#> [56] "Alistipes"
#> [57] "Ruminiclostridium 5"
#> [58] "Cloacibacillus"
#> [59] "Parabacteroides"
#> [60] "Ruminococcaceae UCG-008"
#> [61] "Marvinbryantia"
#> [62] "Mogibacterium"
#> [63] NA
#> [64] "[Eubacterium] ruminantium group"
#> [65] "Erysipelatoclostridium"
#> [66] "Sanguibacteroides"
#> [67] NA
#> [68] NA
#> [69] "Ruminococcaceae UCG-014"
#> [70] NA
#> [71] "Eubacterium"
#> [72] NA
#> [73] "Ruminococcaceae UCG-014"
#> [74] "Turicibacter"
#> [75] NA
#> [76] "Ruminococcus 2"
#> [77] "Lachnoclostridium"
#> [78] NA
#> [79] NA
#> [80] "Actinomyces"
#> [81] "[Eubacterium] oxidoreducens group"
#> [82] NA
#> [83] "Merdibacter"
#> [84] "Ruminococcaceae UCG-014"
#> [85] NA
#> [86] "Bacteroides"
#> [87] NA
#> [88] "Lactobacillus"
#> [89] "Blautia"
#> [90] NA
#> [91] NA
#> [92] NA
#> [93] "Bacteroides"
#> [94] "Ruminococcaceae UCG-010"
#> [95] "Methanobrevibacter"
#> [96] "Defluviitaleaceae UCG-011"
#> [97] NA
#> [98] "Lachnospiraceae UCG-008"
#> [99] NA
#> [100] "GCA-900066575"
#> [101] "[Eubacterium] nodatum group"
#> [102] NA
#> [103] "Barnesiella"
#> [104] "[Eubacterium] coprostanoligenes group"
#> [105] "Lactobacillus"
#> [106] "Ruminococcaceae UCG-014"
#> [107] "Fournierella"
#> [108] "Oscillibacter"
#> [109] "Bacteroides"
#> [110] NA
#> [111] "Christensenellaceae R-7 group"
#> [112] "Ruminococcaceae UCG-005"
#> [113] "Solobacterium"
#> [114] "Prevotella 9"
#> [115] "Holdemania"
#> [116] "Blautia"
#> [117] NA
#> [118] "Dorea"
#> [119] "[Eubacterium] eligens group"
#> [120] "Prevotella 9"
#> [121] NA
#> [122] NA
#> [123] "Ruminococcus 1"
#> [124] "Family XIII AD3011 group"
#> [125] "Parasutterella"
#> [126] "Pseudoflavonifractor"
#> [127] "Lactonifactor"
#> [128] "Flavonifractor"
#> [129] NA
#> [130] "Akkermansia"
#> [131] "Bacteroides"
#> [132] NA
#> [133] "Ruminococcaceae UCG-004"
#> [134] "Lachnospiraceae NC2004 group"
#> [135] "Bacteroides"
#> [136] "Bifidobacterium"
#> [137] "Blautia"
#> [138] "Anaerofilum"
#> [139] NA
#> [140] "UBA1819"
#> [141] "Veillonella"
#> [142] "Flavonifractor"
#> [143] "[Eubacterium] coprostanoligenes group"
#> [144] NA
#> [145] "Ruminococcus 1"
#> [146] "Flavonifractor"
#> [147] "Erysipelotrichaceae UCG-003"
#> [148] "Lachnospiraceae UCG-010"
#> [149] NA
#> [150] "Parabacteroides"
#> [151] "Defluviitaleaceae UCG-011"
#> [152] "Ruminococcaceae UCG-011"
#> [153] "Eisenbergiella"
#> [154] "Butyrivibrio"
#> [155] "Holdemania"
#> [156] NA
#> [157] "Ruminococcaceae UCG-002"
#> [158] "Bacteroides"
#> [159] "Ruminiclostridium 5"
#> [160] "Family XIII AD3011 group"
#> [161] NA
#> [162] NA
#> [163] "GCA-900066225"
#> [164] "Lachnoclostridium"
#> [165] "Butyricicoccus"
#> [166] "Blautia"
#> [167] NA
#> [168] NA
#> [169] "Ruminiclostridium 5"
#> [170] "Veillonella"
#> [171] "Dialister"
#> [172] NA
#> [173] NA
#> [174] "Lachnoclostridium"
#> [175] "Ruminococcaceae UCG-008"
#> [176] NA
#> [177] "Intestinimonas"
#> [178] "Bacteroides"
#> [179] "Bacteroides"
#> [180] NA
#> [181] NA
#> [182] "Ruminiclostridium 9"
#> [183] "Gordonibacter"
#> [184] "Blautia"
#> [185] "Blautia"
#> [186] "Streptococcus"
#> [187] NA
#> [188] "Candidatus Soleaferrea"
#> [189] "Bifidobacterium"
#> [190] NA
#> [191] NA
#> [192] "Fournierella"
#> [193] "Butyricicoccus"
#> [194] "Blautia"
#> [195] NA
#> [196] "Catenibacterium"
#> [197] "Clostridium"
#> [198] NA
#> [199] "Parabacteroides"
#> [200] "Lachnoclostridium"
#> [201] NA
#> [202] "Eubacterium"
#> [203] "[Eubacterium] coprostanoligenes group"
#> [204] NA
#> [205] "Lactococcus"
#> [206] NA
#> [207] "Merdibacter"
#> [208] "Ruminococcaceae UCG-010"
#> [209] "Prevotellaceae NK3B31 group"
#> [210] NA
#> [211] "Paraprevotella"
#> [212] "Lachnospira"
#> [213] NA
#> [214] "Barnesiella"
#> [215] "Ruminococcaceae UCG-005"
#> [216] "Veillonella"
#> [217] NA
#> [218] "Ruminiclostridium 9"
#> [219] NA
#> [220] "Ruminococcaceae UCG-014"
#> [221] NA
#> [222] "Faecalibacterium"
#> [223] "Lachnospiraceae FCS020 group"
#> [224] NA
#> [225] NA
#> [226] NA
#> [227] NA
#> [228] "Erysipelotrichaceae UCG-003"
#> [229] "Ezakiella"
#> [230] "Ruminococcaceae UCG-010"
#> [231] "Lachnoclostridium"
#> [232] "Alistipes"
#> [233] NA
#> [234] NA
#> [235] "Butyricimonas"
#> [236] NA
#> [237] "Ruminiclostridium 6"
#> [238] NA
#> [239] "Butyricimonas"
#> [240] "Christensenellaceae R-7 group"
#> [241] "Butyricimonas"
#> [242] "Butyrivibrio"
#> [243] NA
#> [244] "Family XIII AD3011 group"
#> [245] "Bilophila"
#> [246] "Ruminococcaceae UCG-011"
#> [247] "Intestinibacter"
#> [248] NA
#> [249] "Ruminococcaceae UCG-005"
#> [250] "Victivallis"
#> [251] "Ruminococcaceae V9D2013 group"
#> [252] "Lachnoclostridium"
#> [253] NA
#> [254] "Ruminococcus 1"
#> [255] NA
#> [256] "Blautia"
#> [257] NA
#> [258] NA
#> [259] "Ruminococcus 1"
#> [260] NA
#> [261] "Eubacterium"
#> [262] "Bilophila"
#> [263] NA
#> [264] "Odoribacter"
#> [265] "CAG-873"
#> [266] "Collinsella"
#> [267] "Sporobacter"
#> [268] "Candidatus Soleaferrea"
#> [269] "Halomonas"
#> [270] NA
#> [271] "Blautia"
#> [272] "Ruminococcaceae UCG-011"
#> [273] NA
#> [274] "Oscillibacter"
#> [275] "Eubacterium"
#> [276] NA
#> [277] NA
#> [278] "Ruminiclostridium 5"
#> [279] "Desulfovibrio"
#> [280] "Christensenellaceae R-7 group"
#> [281] "Family XIII AD3011 group"
#> [282] "[Eubacterium] fissicatena group"
#> [283] NA
#> [284] NA
#> [285] "Parabacteroides"
#> [286] "Clostridium"
#> [287] "Ruminiclostridium 9"
#> [288] "Ruminiclostridium 5"
#> [289] "Subdoligranulum"
#> [290] "Lachnospiraceae UCG-001"
#> [291] "Ruminiclostridium 5"
#> [292] "Intestinimonas"
#> [293] "Hungatella"
#> [294] "Klebsiella"
#> [295] "Bacteroides"
#> [296] "Defluviitaleaceae UCG-011"
#> [297] "Ruminococcaceae UCG-013"
#> [298] "Blautia"
#> [299] "Shewanella"
#> [300] NA
#> [301] "Moryella"
#> [302] "Roseburia"
#> [303] "Blautia"
#> [304] "Ruminococcaceae UCG-011"
#> [305] "Bacteroides"
#> [306] "Ruminococcus"
#> [307] NA
#> [308] "Bacteroides"
#> [309] "Ruminococcus 1"
#> [310] "Hydrogenoanaerobacterium"
#> [311] "Ruminococcaceae UCG-003"
#> [312] NA
#> [313] "Blautia"
#> [314] "Lachnospiraceae FCS020 group"
#> [315] NA
#> [316] "[Eubacterium] ventriosum group"
#> [317] "Ruminococcaceae NK4A214 group"
#> [318] NA
#> [319] NA
#> [320] "Sutterella"
#> [321] "Tyzzerella"
#> [322] "Haemophilus"
#> [323] "Roseburia"
#> [324] "Christensenellaceae R-7 group"
#> [325] "Alistipes"
#> [326] "[Eubacterium] hallii group"
#> [327] NA
#> [328] "[Ruminococcus] gauvreauii group"
#> [329] NA
#> [330] "Peptococcus"
#> [331] "Alloprevotella"
#> [332] "Marvinbryantia"
#> [333] NA
#> [334] "Lachnospiraceae UCG-001"
#> [335] "Streptococcus"
#> [336] "Ruminococcaceae UCG-013"
#> [337] NA
#> [338] NA
#> [339] "Pseudoflavonifractor"
#> [340] "Corynebacterium"
#> [341] "Ruminococcus"
#> [342] "Mitsuokella"
#> [343] NA
#> [344] "Ruminococcus"
#> [345] NA
#> [346] "Romboutsia"
#> [347] NA
#> [348] "Alistipes"
#> [349] NA
#> [350] "Actinomyces"
#> [351] "Ruminococcaceae UCG-005"
#> [352] "Intestinimonas"
#> [353] "Ruminococcaceae UCG-002"
#> [354] "Bacteroides"
#> [355] "Erysipelotrichaceae UCG-003"
#> [356] "Oscillibacter"
#> [357] NA
#> [358] "Blautia"
#> [359] "Catabacter"
#> [360] "Erysipelatoclostridium"
#> [361] "Family XIII UCG-001"
#> [362] "Alistipes"
#> [363] "Prevotella"
#> [364] "Rikenellaceae RC9 gut group"
#> [365] "GCA-900066575"
#> [366] "Blautia"
#> [367] NA
#> [368] "Shuttleworthia"
#> [369] NA
#> [370] "Negativibacillus"
#> [371] NA
#> [372] "Clostridium sensu stricto 1"
#> [373] "Family XIII AD3011 group"
#> [374] "Ruminococcus"
#> [375] "Marvinbryantia"
#> [376] NA
#> [377] "Blautia"
#> [378] "Ruminococcus 2"
#> [379] NA
#> [380] NA
#> [381] NA
#> [382] NA
#> [383] NA
#> [384] "Marvinbryantia"
#> [385] NA
#> [386] NA
#> [387] "Ruminococcaceae UCG-005"
#> [388] NA
#> [389] "Ruminiclostridium"
#> [390] "Ruminococcaceae UCG-014"
#> [391] "[Eubacterium] brachy group"
#> [392] "Ruminococcus"
#> [393] "CAG-352"
#> [394] NA
#> [395] "Ruminococcaceae UCG-009"
#> [396] NA
#> [397] "Lachnospiraceae NC2004 group"
#> [398] "Christensenellaceae R-7 group"
#> [399] "Ruminococcaceae UCG-014"
#> [400] "Ruminococcaceae UCG-011"
#> [401] NA
#> [402] "Parabacteroides"
#> [403] "Lachnospiraceae UCG-003"
#> [404] NA
#> [405] "Coprococcus 2"
#> [406] "Lachnoclostridium"
#> [407] "Lachnospiraceae UCG-004"
#> [408] "Oscillibacter"
#> [409] NA
#> [410] NA
#> [411] "Eisenbergiella"
#> [412] NA
#> [413] "Oscillospira"
#> [414] "Holdemanella"
#> [415] NA
#> [416] "Butyricimonas"
#> [417] "Lachnoclostridium"
#> [418] "Ruminococcaceae UCG-005"
#> [419] NA
#> [420] NA
#> [421] "Dorea"
#> [422] "Lachnospiraceae UCG-002"
#> [423] "Roseburia"
#> [424] "Staphylococcus"
#> [425] "Subdoligranulum"
#> [426] NA
#> [427] NA
#> [428] NA
#> [429] "[Eubacterium] xylanophilum group"
#> [430] "Ruminococcus 1"
#> [431] NA
#> [432] "Ruminiclostridium 9"
#> [433] "Lachnoclostridium"
#> [434] NA
#> [435] "[Eubacterium] ventriosum group"
#> [436] "Bacteroides"
#> [437] "Victivallis"
#> [438] NA
#> [439] "Streptococcus"
#> [440] "Bacteroides"
#> [441] NA
#> [442] "Blautia"
#> [443] "Oribacterium"
#> [444] NA
#> [445] "Parabacteroides"
#> [446] "[Eubacterium] hallii group"
#> [447] "Ruminococcaceae UCG-009"
#> [448] "Alistipes"
#> [449] "Shuttleworthia"
#> [450] NA
#> [451] NA
#> [452] "Tyzzerella"
#> [453] "Roseburia"
#> [454] "Lachnospira"
#> [455] NA
#> [456] NA
#> [457] "Ruminiclostridium 9"
#> [458] "Alistipes"
#> [459] NA
#> [460] NA
#> [461] "Lachnospiraceae UCG-008"
#> [462] NA
#> [463] NA
#> [464] "Methanobrevibacter"
#> [465] "Christensenellaceae R-7 group"
#> [466] "Blautia"
#> [467] NA
#> [468] "Epulopiscium"
#> [469] "Eisenbergiella"
#> [470] NA
#> [471] NA
#> [472] NA
#> [473] NA
#> [474] "[Eubacterium] coprostanoligenes group"
#> [475] "Ruminococcaceae UCG-005"
#> [476] "Streptococcus"
#> [477] "Lachnospiraceae UCG-004"
#> [478] "Ruminococcaceae UCG-005"
#> [479] "Parabacteroides"
#> [480] "Clostridium"
#> [481] NA
#> [482] NA
#> [483] NA
#> [484] "Ruminococcaceae UCG-014"
#> [485] "Intestinimonas"
#> [486] NA
#> [487] "Bacteroides"
#> [488] NA
#> [489] "Lactobacillus"
#> [490] NA
#> [491] "Acetanaerobacterium"
#> [492] "Ruminococcaceae UCG-005"
#> [493] "Ruminococcus"
#> [494] NA
#> [495] NA
#> [496] NA
#> [497] "Lachnospiraceae UCG-004"
#> [498] NA
#> [499] "Butyricimonas"
#> [500] "Ruminococcaceae UCG-002"
#> [501] "Ruminococcaceae UCG-010"
#> [502] "Anaerosporobacter"
#> [503] "Paraprevotella"
#> [504] "Eubacterium"
#> [505] "Blautia"
#> [506] "Lachnospiraceae FCS020 group"
#> [507] NA
#> [508] "Family XIII AD3011 group"
#> [509] "Ruminococcaceae UCG-007"
#> [510] NA
#> [511] "Bifidobacterium"
#> [512] "Negativibacillus"
#> [513] "Roseburia"
#> [514] "Christensenellaceae R-7 group"
#> [515] "Lachnospiraceae ND3007 group"
#> [516] "Blautia"
#> [517] "Ruminococcaceae UCG-014"
#> [518] "Actinomyces"
#> [519] "Ruminococcaceae UCG-003"
#> [520] "Lachnoclostridium"
#> [521] "Paraprevotella"
#> [522] NA
#> [523] "[Eubacterium] hallii group"
#> [524] "Lachnospiraceae NC2004 group"
#> [525] "Ruminococcaceae UCG-014"
#> [526] "Faecalibacterium"
#> [527] NA
#> [528] NA
#> [529] "Ruminococcaceae UCG-014"
#> [530] "[Eubacterium] coprostanoligenes group"
#> [531] "Ruminococcaceae UCG-009"
#> [532] NA
#> [533] "Ruminococcus 1"
#> [534] NA
#> [535] "[Eubacterium] xylanophilum group"
#> [536] "Romboutsia"
#> [537] "Holdemanella"
#> [538] "Ruminococcus"
#> [539] "Paraprevotella"
#> [540] NA
#> [541] "Oscillibacter"
#> [542] "Streptococcus"
#> [543] "Alistipes"
#> [544] NA
#> [545] "Ruminiclostridium 9"
#> [546] "Prevotella 7"
#> [547] NA
#> [548] "Roseburia"
#> [549] "Blautia"
#> [550] "Lachnospiraceae UCG-001"
#> [551] NA
#> [552] "Anaerotruncus"
#> [553] NA
#> [554] NA
#> [555] NA
#> [556] "Sutterella"
#> [557] "Ruminococcaceae NK4A214 group"
#> [558] NA
#> [559] NA
#> [560] "Ruminococcus"
#> [561] NA
#> [562] "Peptococcus"
#> [563] "Blautia"
#> [564] NA
#> [565] NA
#> [566] "Flavonifractor"
#> [567] "Ruminococcaceae UCG-013"
#> [568] "Phocea"
#> [569] NA
#> [570] NA
#> [571] "Catabacter"
#> [572] NA
#> [573] "Phascolarctobacterium"
#> [574] NA
#> [575] "Terrisporobacter"
#> [576] NA
#> [577] "Negativibacillus"
#> [578] NA
#> [579] NA
#> [580] "Methanosphaera"
#> [581] NA
#> [582] NA
#> [583] "Methanobrevibacter"
#> [584] "UC5-1-2E3"
#> [585] "Ruminococcaceae UCG-003"
#> [586] "Ruminococcus 1"
#> [587] "Faecalibacterium"
#> [588] NA
#> [589] NA
#> [590] "Paraprevotella"
#> [591] NA
#> [592] "Oscillospira"
#> [593] "Christensenellaceae R-7 group"
#> [594] NA
#> [595] "Coprococcus 2"
#> [596] "Holdemania"
#> [597] NA
#> [598] "Peptococcus"
#> [599] NA
#> [600] "Rothia"
#> [601] NA
#> [602] "Lactobacillus"
#> [603] "Ruminococcaceae NK4A214 group"
#> [604] NA
#> [605] "Eubacterium"
#> [606] NA
#> [607] NA
#> [608] "Ruminiclostridium 6"
#> [609] NA
#> [610] "Alistipes"
#> [611] "Merdibacter"
#> [612] "Butyricimonas"
#> [613] NA
#> [614] "Allisonella"
#> [615] NA
#> [616] "Ruminococcaceae UCG-011"
#> [617] NA
#> [618] NA
#> [619] "Coprobacter"
#> [620] "Barnesiella"
#> [621] "Olsenella"
#> [622] "Bacteroides"
#> [623] "Family XIII AD3011 group"
#> [624] "Ruminococcaceae NK4A214 group"
#> [625] "Prevotella 9"
#> [626] "Clostridium"
#> [627] NA
#> [628] NA
#> [629] NA
#> [630] "Undibacterium"
#> [631] "Lactobacillus"
#> [632] NA
#> [633] NA
#> [634] "Harryflintia"
#> [635] NA
#> [636] "Blautia"
#> [637] "[Eubacterium] hallii group"
#> [638] NA
#> [639] "Ruminococcus 1"
#> [640] "Oscillibacter"
#> [641] "[Eubacterium] coprostanoligenes group"
#> [642] "Butyricicoccus"
#> [643] NA
#> [644] "Actinomyces"
#> [645] "Anaerostipes"
#> [646] NA
#> [647] NA
#> [648] NA
#> [649] "DTU089"
#> [650] "Clostridium"
#> [651] "Alistipes"
#> [652] NA
#> [653] "Family XIII UCG-001"
#> [654] NA
#> [655] NA
#> [656] "Escherichia/Shigella"
#> [657] "Enterorhabdus"
#> [658] NA
#> [659] "Blautia"
#> [660] NA
#> [661] "Anaerosporobacter"
#> [662] "CHKCI001"
#> [663] "Family XIII AD3011 group"
#> [664] NA
#> [665] NA
#> [666] NA
#> [667] "Ralstonia"
#> [668] "Lachnospiraceae NC2004 group"
#> [669] "Ruminococcaceae UCG-014"
#> [670] NA
#> [671] NA
#> [672] "Alistipes"
#> [673] NA
#> [674] "Bacteroides"
#> [675] "Ruminococcaceae UCG-011"
#> [676] NA
#> [677] "Alistipes"
#> [678] NA
#> [679] "Dialister"
#> [680] "Tyzzerella 4"
#> [681] NA
#> [682] NA
#> [683] NA
#> [684] NA
#> [685] "Collinsella"
#> [686] "Ruminococcaceae UCG-010"
#> [687] "[Eubacterium] coprostanoligenes group"
#> [688] "Lactobacillus"
#> [689] "Lachnospiraceae UCG-004"
#> [690] "Anaerofilum"
#> [691] NA
#> [692] "Romboutsia"
#> [693] "Blautia"
#> [694] "Coriobacteriaceae UCG-002"
#> [695] NA
#> [696] "Ruminococcaceae UCG-002"
#> [697] NA
#> [698] "Rothia"
#> [699] "GCA-900066225"
#> [700] "Anaeroplasma"
#> [701] NA
#> [702] "Blautia"
#> [703] "Bacteroides"
#> [704] NA
#> [705] "Lachnoclostridium"
#> [706] "Terrisporobacter"
#> [707] NA
#> [708] NA
#> [709] NA
#> [710] "Lactobacillus"
#> [711] "Lachnotalea"
#> [712] "Erysipelatoclostridium"
#> [713] "Roseburia"
#> [714] "Leuconostoc"
#> [715] "Blautia"
#> [716] NA
#> [717] "Ruminiclostridium 9"
#> [718] NA
#> [719] "Sutterella"
#> [720] NA
#> [721] "UBA1819"
#> [722] NA
#> [723] "Ruminiclostridium 5"
#> [724] "Ruminococcaceae UCG-014"
#> [725] "Christensenella"
#> [726] "Anaerofustis"
#> [727] NA
#> [728] NA
#> [729] "Victivallis"
#> [730] NA
#> [731] "Ruminiclostridium 5"
#> [732] "Lachnoclostridium"
#> [733] NA
#> [734] "Ruminococcaceae NK4A214 group"
#> [735] NA
#> [736] "Butyricicoccus"
#> [737] "Lachnoclostridium"
#> [738] "Lachnospiraceae UCG-001"
#> [739] NA
#> [740] NA
#> [741] "Ruminococcaceae UCG-011"
#> [742] NA
#> [743] NA
#> [744] NA
#> [745] NA
#> [746] "Ruminococcaceae UCG-010"
#> [747] "Slackia"
#> [748] NA
#> [749] NA
#> [750] "Lachnoclostridium"
#> [751] "Coprococcus"
#> [752] "Ruminococcaceae UCG-014"
#> [753] "Bacteroides"
#> [754] NA
#> [755] "Roseburia"
#> [756] "Oscillospira"
#> [757] "Negativibacillus"
#> [758] "Blautia"
#> [759] "Streptococcus"
#> [760] NA
#> [761] "Faecalibacterium"
#> [762] NA
#> [763] NA
#> [764] "Christensenellaceae R-7 group"
#> [765] "Sarcina"
#> [766] "Christensenellaceae R-7 group"
#> [767] NA
#> [768] "Oscillibacter"
#> [769] "Pseudoflavonifractor"
#> [770] "Howardella"
#> [771] "Family XIII AD3011 group"
#> [772] NA
#> [773] "Blautia"
#> [774] NA
#> [775] "Ruminococcaceae UCG-002"
#> [776] "Hungatella"
#> [777] NA
#> [778] "Coprococcus"
#> [779] "Ruminococcaceae NK4A214 group"
#> [780] "Ruminococcaceae NK4A214 group"
#> [781] NA
#> [782] NA
#> [783] "Oscillospira"
#> [784] "Defluviitaleaceae UCG-011"
#> [785] "Bacteroides"
#> [786] "Sporobacter"
#> [787] "Roseburia"
#> [788] "Erysipelotrichaceae UCG-003"
#> [789] "[Ruminococcus] gauvreauii group"
#> [790] "Lachnospiraceae ND3007 group"
#> [791] "Anaerostipes"
#> [792] NA
#> [793] NA
#> [794] "Ruminococcus"
#> [795] "Oxalobacter"
#> [796] NA
#> [797] NA
#> [798] NA
#> [799] "[Eubacterium] eligens group"
#> [800] NA
#> [801] NA
#> [802] "Alistipes"
#> [803] "Bifidobacterium"
#> [804] NA
#> [805] "Butyricicoccus"
#> [806] "[Ruminococcus] gauvreauii group"
#> [807] NA
#> [808] "Lachnospiraceae NC2004 group"
#> [809] "Ruminiclostridium 9"
#> [810] "Leuconostoc"
#> [811] NA
#> [812] NA
#> [813] "Ruminiclostridium 9"
#> [814] "Turicibacter"
#> [815] NA
#> [816] NA
#> [817] "Alistipes"
#> [818] "Bacteroides"
#> [819] NA
#> [820] NA
#> [821] NA
#> [822] "Bacteroides"
#> [823] "Oscillospira"
#> [824] "Anaerofilum"
#> [825] "Lachnospiraceae UCG-010"
#> [826] "Eubacterium"
#> [827] "Blautia"
#> [828] "Desulfovibrio"
#> [829] "Veillonella"
#> [830] NA
#> [831] "Clostridium"
#> [832] "Halomonas"
#> [833] "Ruminococcaceae UCG-013"
#> [834] NA
#> [835] NA
#> [836] "Ruminococcaceae UCG-009"
#> [837] "Bacteroides"
#> [838] "Eisenbergiella"
#> [839] "Papillibacter"
#> [840] "Blautia"
#> [841] "GCA-900066755"
#> [842] NA
#> [843] "Ruminococcaceae UCG-010"
#> [844] "Parabacteroides"
#> [845] "Lachnospiraceae ND3007 group"
#> [846] "Ruminiclostridium 5"
#> [847] NA
#> [848] "Ruminococcaceae UCG-005"
#> [849] "Holdemanella"
#> [850] NA
#> [851] "Ruminococcus"
#> [852] NA
#> [853] NA
#> [854] "Christensenellaceae R-7 group"
#> [855] NA
#> [856] "[Ruminococcus] gauvreauii group"
#> [857] "Ruminococcaceae NK4A214 group"
#> [858] NA
#> [859] NA
#> [860] "Parabacteroides"
#> [861] "Intestinimonas"
#> [862] "Ruminococcaceae UCG-004"
#> [863] "[Eubacterium] hallii group"
#> [864] NA
#> [865] NA
#> [866] "Ruminiclostridium"
#> [867] "Blautia"
#> [868] "Bacteroides"
#> [869] "Faecalibacterium"
#> [870] "Sellimonas"
#> [871] "Butyricimonas"
#> [872] "Ruminococcaceae UCG-008"
#> [873] "Senegalimassilia"
#> [874] "Faecalitalea"
#> [875] NA
#> [876] "Desulfovibrio"
#> [877] NA
#> [878] NA
#> [879] "Blautia"
#> [880] "Coprococcus"
#> [881] "Ruminococcaceae UCG-014"
#> [882] "Defluviitaleaceae UCG-011"
#> [883] "Erysipelatoclostridium"
#> [884] "Olsenella"
#> [885] NA
#> [886] "Erysipelotrichaceae UCG-003"
#> [887] "Family XIII UCG-001"
#> [888] NA
#> [889] "Ruminococcaceae UCG-011"
#> [890] NA
#> [891] NA
#> [892] "Fusicatenibacter"
#> [893] "GCA-900066225"
#> [894] "Lachnospiraceae UCG-010"
#> [895] "Roseburia"
#> [896] "Ruminococcus"
#> [897] "Roseburia"
#> [898] "Butyricicoccus"
#> [899] "Ruminococcaceae UCG-014"
#> [900] "Bacteroides"
#> [901] "Lactobacillus"
#> [902] "Prevotella 9"
#> [903] "Anaerotruncus"
#> [904] "Lachnoclostridium"
#> [905] "[Eubacterium] eligens group"