This analysis pipe noted https://f1000research.com/articles/5-1492.
Roading the data
from previous lecture.. we generated a phyloseq object. it can be saved to hard disk using the below command.
saveRDS(ps, "phyloseq_example.rds")
And it can be loaded to a new R session like below!
library(phyloseq)
library(tidyverse)
library(microbiome)
library(vegan)
phyloseq <- readRDS("phyloseq_example.rds")Phyloseq object
phyloseq is a list - list of multiple objects such as
sample_data, otu_table,
tax_table, etc.
phyloseq## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 225 taxa and 19 samples ]
## sample_data() Sample Data: [ 19 samples by 4 sample variables ]
## tax_table() Taxonomy Table: [ 225 taxa by 6 taxonomic ranks ]
## refseq() DNAStringSet: [ 225 reference sequences ]using sample_data() function, we can extract
sample_data only from a phyloseq object
sample_data(phyloseq)## Subject Gender Day When
## F3D0 3 F 0 Early
## F3D1 3 F 1 Early
## F3D141 3 F 141 Late
## F3D142 3 F 142 Late
## F3D143 3 F 143 Late
## F3D144 3 F 144 Late
## F3D145 3 F 145 Late
## F3D146 3 F 146 Late
## F3D147 3 F 147 Late
## F3D148 3 F 148 Late
## F3D149 3 F 149 Late
## F3D150 3 F 150 Late
## F3D2 3 F 2 Early
## F3D3 3 F 3 Early
## F3D5 3 F 5 Early
## F3D6 3 F 6 Early
## F3D7 3 F 7 Early
## F3D8 3 F 8 Early
## F3D9 3 F 9 Early#or
phyloseq %>%sample_data()## Subject Gender Day When
## F3D0 3 F 0 Early
## F3D1 3 F 1 Early
## F3D141 3 F 141 Late
## F3D142 3 F 142 Late
## F3D143 3 F 143 Late
## F3D144 3 F 144 Late
## F3D145 3 F 145 Late
## F3D146 3 F 146 Late
## F3D147 3 F 147 Late
## F3D148 3 F 148 Late
## F3D149 3 F 149 Late
## F3D150 3 F 150 Late
## F3D2 3 F 2 Early
## F3D3 3 F 3 Early
## F3D5 3 F 5 Early
## F3D6 3 F 6 Early
## F3D7 3 F 7 Early
## F3D8 3 F 8 Early
## F3D9 3 F 9 EarlyNote that sample_data object is different from
data_frame. However it can be converted into data_frame as
below
phyloseq %>% sample_data() %>% data.frame()## Subject Gender Day When
## F3D0 3 F 0 Early
## F3D1 3 F 1 Early
## F3D141 3 F 141 Late
## F3D142 3 F 142 Late
## F3D143 3 F 143 Late
## F3D144 3 F 144 Late
## F3D145 3 F 145 Late
## F3D146 3 F 146 Late
## F3D147 3 F 147 Late
## F3D148 3 F 148 Late
## F3D149 3 F 149 Late
## F3D150 3 F 150 Late
## F3D2 3 F 2 Early
## F3D3 3 F 3 Early
## F3D5 3 F 5 Early
## F3D6 3 F 6 Early
## F3D7 3 F 7 Early
## F3D8 3 F 8 Early
## F3D9 3 F 9 EarlyThis is dataframe. You can manipulate it as you want.
OTU table
otu_table object can be pulled out using
otu_table() function. It is about the abundance (read
counts) of each taxa, by sample
otu_table(phyloseq)## OTU Table: [225 taxa and 19 samples]
## taxa are columns
## ASV1 ASV2 ASV3 ASV4 ASV5 ASV6 ASV7 ASV8 ASV9 ASV10 ASV11 ASV12 ASV13
## F3D0 577 345 444 427 154 467 282 183 44 158 16 217 52
## F3D1 404 352 231 68 135 41 96 187 69 106 91 40 127
## F3D141 443 361 340 495 188 325 243 320 166 130 145 145 12
## F3D142 288 303 158 162 178 181 163 89 89 78 41 98 99
## F3D143 230 174 202 230 128 243 152 81 108 68 68 110 43
## F3D144 416 275 301 356 103 353 240 41 158 154 245 145 16
## F3D145 643 488 519 578 301 473 396 125 198 229 292 253 20
## F3D146 325 230 250 389 178 274 212 71 112 88 161 145 4
## F3D147 1489 1213 907 1084 450 1168 853 74 765 267 409 559 143
## F3D148 858 728 575 849 437 871 577 501 404 196 365 430 17
## F3D149 879 778 716 895 415 631 559 510 418 286 429 298 87
## F3D150 314 230 397 467 168 213 231 118 245 149 59 98 64
## F3D2 3479 1575 1167 468 335 115 324 1199 433 614 52 41 324
## F3D3 983 601 464 197 399 25 166 375 307 296 152 0 94
## F3D5 327 270 283 158 151 22 122 205 175 207 53 0 48
## F3D6 1008 671 583 399 473 17 278 259 202 239 39 0 420
## F3D7 644 507 432 311 466 11 195 211 174 270 15 0 115
## F3D8 276 349 348 146 553 0 130 286 112 196 17 0 145
## F3D9 510 420 479 205 592 0 207 437 145 224 26 0 181
## ASV14 ASV15 ASV16 ASV17 ASV18 ASV19 ASV20 ASV21 ASV22 ASV23 ASV24 ASV25
## F3D0 104 91 78 99 68 67 65 41 44 53 26 70
## F3D1 28 320 0 0 31 108 0 52 14 135 8 69
## F3D141 65 33 103 149 43 6 0 45 85 15 57 0
## F3D142 64 12 52 116 30 6 0 0 34 6 14 0
## F3D143 61 9 40 0 20 0 0 12 65 0 0 0
## F3D144 81 11 113 0 44 5 0 45 17 0 13 0
## F3D145 121 15 123 194 104 5 120 39 13 8 20 0
## F3D146 58 25 35 0 35 0 78 16 77 47 16 19
## F3D147 290 74 303 251 141 41 339 128 79 0 109 9
## F3D148 198 56 269 256 117 55 270 110 94 52 181 12
## F3D149 161 42 177 82 119 4 233 146 262 0 102 8
## F3D150 74 19 29 85 49 5 0 19 143 23 53 6
## F3D2 107 367 17 69 191 399 44 30 17 293 34 333
## F3D3 60 46 24 0 105 342 0 121 0 0 22 43
## F3D5 38 87 35 57 37 17 19 10 0 55 25 57
## F3D6 106 57 0 0 39 74 12 29 0 37 26 66
## F3D7 73 39 0 0 22 39 10 38 0 30 48 13
## F3D8 65 44 6 0 21 20 0 111 0 36 22 57
## F3D9 72 98 0 0 38 42 0 24 0 49 39 44
## ASV26 ASV27 ASV28 ASV29 ASV30 ASV31 ASV32 ASV33 ASV34 ASV35 ASV36 ASV37
## F3D0 74 31 61 57 43 262 27 74 0 34 45 56
## F3D1 100 45 25 140 119 56 29 72 0 101 54 52
## F3D141 0 9 12 0 35 50 57 22 0 0 0 20
## F3D142 0 0 21 0 0 12 8 10 0 0 4 0
## F3D143 0 14 22 0 4 0 24 13 0 0 0 0
## F3D144 0 19 0 0 10 14 10 16 0 0 0 16
## F3D145 6 18 0 0 11 0 18 12 0 0 0 19
## F3D146 36 36 0 0 35 18 22 22 0 0 0 26
## F3D147 34 33 51 14 17 0 48 12 0 0 25 24
## F3D148 8 14 57 0 22 21 44 9 0 0 0 17
## F3D149 7 46 46 23 36 0 143 43 0 0 12 52
## F3D150 6 32 35 0 0 0 81 31 0 0 0 25
## F3D2 200 146 59 281 108 137 41 82 0 184 112 56
## F3D3 15 20 22 20 8 0 9 8 0 9 12 20
## F3D5 52 49 77 34 45 35 0 40 0 16 48 21
## F3D6 107 47 42 40 19 0 20 46 0 23 52 45
## F3D7 48 13 35 0 8 0 0 7 0 12 20 0
## F3D8 40 44 61 0 49 0 8 30 0 71 57 43
## F3D9 52 63 52 56 93 28 15 40 0 95 96 33
## ASV38 ASV39 ASV40 ASV41 ASV42 ASV43 ASV44 ASV45 ASV46 ASV47 ASV48 ASV49
## F3D0 5 27 18 32 0 50 10 0 0 0 8 42
## F3D1 14 34 20 71 0 63 19 0 72 0 22 54
## F3D141 31 26 13 0 0 18 0 0 8 62 19 0
## F3D142 0 12 0 0 0 0 0 0 0 0 0 0
## F3D143 12 14 11 0 0 8 0 0 0 0 14 0
## F3D144 17 0 0 0 0 0 0 0 0 37 0 0
## F3D145 16 0 6 0 5 0 0 0 0 46 0 0
## F3D146 13 32 23 0 0 21 0 0 11 93 14 0
## F3D147 44 43 38 0 0 12 13 0 11 37 42 0
## F3D148 20 50 21 0 0 14 9 0 15 12 34 0
## F3D149 59 87 44 0 0 45 21 0 34 0 63 0
## F3D150 53 29 40 0 0 25 0 0 16 0 20 0
## F3D2 94 41 82 81 0 89 79 0 55 0 73 138
## F3D3 17 9 7 15 0 28 20 0 10 0 0 10
## F3D5 33 10 18 33 0 7 36 0 52 0 6 11
## F3D6 31 28 21 51 0 0 37 0 25 14 7 26
## F3D7 9 11 10 23 0 0 32 0 8 0 7 9
## F3D8 24 5 21 38 0 9 42 0 16 23 11 42
## F3D9 32 16 31 63 0 0 58 0 29 36 17 24
## ASV50 ASV51 ASV52 ASV53 ASV54 ASV55 ASV56 ASV57 ASV58 ASV59 ASV60 ASV61
## F3D0 33 0 51 5 0 0 48 13 18 83 0 0
## F3D1 45 0 45 11 0 32 23 21 34 48 0 0
## F3D141 0 0 0 8 18 40 0 0 28 0 0 29
## F3D142 0 0 0 8 10 0 6 0 0 0 0 23
## F3D143 0 0 0 7 0 36 8 0 0 0 0 24
## F3D144 0 0 0 8 22 0 14 0 0 0 0 16
## F3D145 0 0 0 20 13 12 11 0 0 3 0 18
## F3D146 0 0 0 5 37 29 20 0 16 0 0 5
## F3D147 11 0 0 37 89 17 30 18 28 26 0 55
## F3D148 0 0 0 13 62 43 23 0 22 0 0 94
## F3D149 7 0 8 12 43 28 35 0 27 0 0 34
## F3D150 0 0 0 8 41 19 15 0 15 0 0 14
## F3D2 151 0 107 55 0 0 38 44 48 81 0 0
## F3D3 6 0 0 43 0 0 0 0 0 15 0 0
## F3D5 9 0 52 6 0 20 20 22 19 0 0 0
## F3D6 44 0 11 23 0 0 19 30 22 6 0 0
## F3D7 12 0 0 26 0 0 0 20 0 19 0 0
## F3D8 13 0 36 21 0 26 6 56 23 11 0 0
## F3D9 23 0 33 26 0 31 14 104 23 30 0 0
## ASV62 ASV63 ASV64 ASV65 ASV66 ASV67 ASV68 ASV69 ASV70 ASV71 ASV72 ASV73
## F3D0 60 0 0 0 46 23 19 19 0 0 41 0
## F3D1 53 0 0 37 38 0 19 52 0 0 41 10
## F3D141 0 0 0 6 0 16 13 0 0 45 10 16
## F3D142 0 0 0 0 0 28 0 0 0 0 0 0
## F3D143 0 3 0 6 0 10 4 0 0 22 0 13
## F3D144 0 0 2 0 0 21 0 0 0 0 0 0
## F3D145 0 5 4 10 0 7 5 0 0 0 0 0
## F3D146 0 0 0 13 18 3 15 0 0 11 0 12
## F3D147 0 0 0 0 23 28 13 0 0 18 8 0
## F3D148 0 0 0 10 0 71 18 0 0 18 0 14
## F3D149 0 0 0 13 0 28 59 0 0 82 19 67
## F3D150 0 0 0 12 0 19 23 0 0 46 0 18
## F3D2 79 0 0 81 38 4 47 79 0 0 99 32
## F3D3 12 0 0 10 0 16 5 0 0 0 17 9
## F3D5 34 0 0 18 0 0 6 25 0 0 0 0
## F3D6 51 0 0 12 63 0 9 41 0 0 0 15
## F3D7 20 0 0 0 0 0 0 0 0 0 0 8
## F3D8 0 0 0 31 20 0 13 36 0 0 0 7
## F3D9 0 0 0 28 28 0 6 21 0 0 0 12
## ASV74 ASV75 ASV76 ASV77 ASV78 ASV79 ASV80 ASV81 ASV82 ASV83 ASV84 ASV85
## F3D0 92 128 0 0 10 0 25 0 5 0 14 0
## F3D1 12 0 11 0 11 0 3 15 20 0 0 2
## F3D141 22 6 0 30 0 0 15 7 12 0 0 0
## F3D142 0 4 0 0 0 0 0 0 0 0 0 0
## F3D143 20 0 0 15 0 11 0 0 8 0 0 0
## F3D144 0 6 0 0 0 10 0 0 0 0 0 0
## F3D145 0 14 5 0 0 0 0 9 0 0 0 0
## F3D146 0 0 12 9 7 0 6 19 11 0 0 0
## F3D147 0 18 0 25 64 45 11 18 41 0 11 5
## F3D148 0 31 0 21 18 12 16 5 0 0 23 0
## F3D149 0 13 8 73 24 0 14 13 26 0 19 0
## F3D150 0 6 4 51 0 30 0 12 11 0 0 0
## F3D2 35 0 20 0 16 0 37 37 12 0 29 5
## F3D3 0 0 21 0 0 0 19 0 6 0 0 0
## F3D5 0 0 15 0 8 0 11 13 12 0 23 4
## F3D6 15 0 30 0 38 0 9 17 12 0 18 0
## F3D7 0 0 14 0 0 0 19 5 7 0 10 2
## F3D8 17 0 37 0 6 41 8 13 12 0 17 3
## F3D9 15 0 48 0 12 64 17 25 12 0 38 0
## ASV86 ASV87 ASV88 ASV89 ASV90 ASV91 ASV92 ASV93 ASV94 ASV95 ASV96 ASV97
## F3D0 6 24 0 0 50 0 17 0 0 6 0 0
## F3D1 14 11 0 0 48 0 0 19 30 0 43 0
## F3D141 9 0 0 0 0 0 0 0 0 13 0 12
## F3D142 13 0 0 0 0 0 0 15 0 5 0 0
## F3D143 11 0 0 0 0 0 14 0 0 0 0 6
## F3D144 0 0 0 0 0 0 0 14 0 0 0 10
## F3D145 16 0 0 21 0 0 9 0 3 13 0 13
## F3D146 0 13 34 0 0 0 0 26 3 13 0 13
## F3D147 34 9 20 0 0 0 24 33 17 0 0 11
## F3D148 20 0 16 37 0 0 0 13 17 32 0 23
## F3D149 20 0 14 0 0 0 0 17 7 31 0 42
## F3D150 0 0 0 0 0 0 0 0 0 26 0 12
## F3D2 23 46 0 38 61 0 42 38 5 9 76 0
## F3D3 0 0 0 0 0 0 0 0 15 0 0 0
## F3D5 5 12 0 54 20 0 13 0 18 10 0 6
## F3D6 13 31 0 34 0 0 11 0 16 0 0 10
## F3D7 0 0 6 0 0 0 0 0 18 0 6 0
## F3D8 6 21 46 0 0 0 17 0 13 0 35 0
## F3D9 7 24 52 0 0 0 28 0 9 6 0 0
## ASV98 ASV99 ASV100 ASV101 ASV102 ASV103 ASV104 ASV105 ASV106 ASV107
## F3D0 0 0 0 0 0 0 0 24 3 0
## F3D1 0 0 0 4 0 0 0 0 7 0
## F3D141 0 0 10 8 0 0 19 0 0 0
## F3D142 0 0 6 0 0 0 7 0 0 0
## F3D143 0 0 0 0 0 0 6 0 0 0
## F3D144 0 0 0 3 0 0 6 0 0 0
## F3D145 0 0 0 5 0 0 0 0 0 2
## F3D146 0 0 13 14 0 0 16 8 0 0
## F3D147 0 67 14 11 0 0 30 0 0 0
## F3D148 0 0 19 8 0 0 14 0 0 0
## F3D149 0 27 60 23 0 0 0 5 0 0
## F3D150 0 0 23 11 0 0 10 0 0 0
## F3D2 0 53 0 19 0 0 23 18 31 0
## F3D3 0 0 0 6 0 0 0 0 2 0
## F3D5 0 0 0 6 0 0 0 0 0 0
## F3D6 0 0 0 5 0 0 0 24 19 0
## F3D7 0 0 0 0 0 0 0 0 8 0
## F3D8 0 0 0 9 0 0 0 14 25 0
## F3D9 0 0 0 8 0 0 0 25 19 0
## ASV108 ASV109 ASV110 ASV111 ASV112 ASV113 ASV114 ASV115 ASV116 ASV117
## F3D0 0 0 0 0 6 0 19 0 0 10
## F3D1 0 8 0 0 24 0 23 0 0 0
## F3D141 14 0 14 0 11 0 0 0 0 3
## F3D142 5 0 0 0 0 0 0 11 0 7
## F3D143 6 0 5 0 0 0 0 0 0 6
## F3D144 6 0 10 0 0 0 0 12 0 0
## F3D145 10 0 0 0 0 0 0 16 0 6
## F3D146 13 0 13 13 0 0 0 11 0 16
## F3D147 0 0 0 15 0 0 0 11 0 13
## F3D148 15 0 0 6 0 0 0 12 0 13
## F3D149 24 0 34 41 19 0 0 0 8 9
## F3D150 10 0 17 23 8 0 0 9 0 5
## F3D2 0 26 8 0 21 0 32 0 37 3
## F3D3 0 5 0 0 0 0 0 0 22 0
## F3D5 6 11 0 0 0 0 0 0 16 0
## F3D6 0 29 0 0 0 0 0 0 11 0
## F3D7 0 7 0 0 0 0 11 2 0 0
## F3D8 0 11 0 0 7 0 10 11 0 0
## F3D9 0 8 0 0 0 0 0 0 0 0
## ASV118 ASV119 ASV120 ASV121 ASV122 ASV123 ASV124 ASV125 ASV126 ASV127
## F3D0 10 0 0 34 0 16 0 9 9 0
## F3D1 6 0 0 14 0 15 0 7 17 0
## F3D141 0 0 0 0 10 0 11 0 0 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 12 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 4 0 0 0 0 0 0 0 0
## F3D146 0 0 17 0 11 0 0 0 0 0
## F3D147 13 0 0 0 8 10 0 0 0 18
## F3D148 0 0 0 0 9 0 0 0 0 0
## F3D149 11 0 0 0 32 17 26 0 0 0
## F3D150 9 13 0 0 18 10 11 0 0 0
## F3D2 12 0 20 40 0 0 12 35 46 65
## F3D3 0 0 0 0 0 0 12 12 0 0
## F3D5 5 44 0 0 0 0 0 0 0 0
## F3D6 8 29 20 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 9 0 0 0 0 16 0 9 11 0
## F3D9 7 0 33 0 0 0 0 11 0 0
## ASV128 ASV129 ASV130 ASV131 ASV132 ASV133 ASV134 ASV135 ASV136 ASV137
## F3D0 0 19 0 0 19 11 0 7 0 17
## F3D1 0 17 0 0 7 0 0 0 0 11
## F3D141 0 0 0 13 0 0 0 6 6 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 8 0 0 0 0
## F3D146 0 7 0 0 11 0 12 0 0 0
## F3D147 0 0 0 0 0 15 13 0 0 0
## F3D148 24 0 0 0 0 0 11 0 11 0
## F3D149 43 0 0 0 0 0 12 0 17 0
## F3D150 12 0 0 0 0 0 0 0 0 0
## F3D2 0 30 0 13 10 28 0 39 0 21
## F3D3 0 0 5 0 0 0 0 0 0 0
## F3D5 0 0 0 0 10 0 0 9 0 0
## F3D6 0 0 19 0 0 0 14 0 0 9
## F3D7 0 0 16 0 0 0 0 0 0 0
## F3D8 0 0 13 17 0 0 0 0 10 0
## F3D9 0 0 14 22 7 0 0 0 15 0
## ASV138 ASV139 ASV140 ASV141 ASV142 ASV143 ASV144 ASV145 ASV146 ASV147
## F3D0 0 57 0 16 8 0 0 0 0 0
## F3D1 0 0 7 0 7 0 0 0 0 3
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 3 0 0 0 0 0 0 0 0 0
## F3D143 10 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 15 0 0 0 2 8 0 0 0 0
## F3D146 0 0 0 0 0 0 0 0 0 0
## F3D147 15 0 0 0 0 0 0 25 9 0
## F3D148 11 0 0 0 5 0 0 0 0 0
## F3D149 4 0 10 0 0 21 0 0 26 0
## F3D150 0 0 0 0 0 23 0 0 15 0
## F3D2 0 0 7 14 14 0 0 0 0 8
## F3D3 0 0 0 0 0 0 0 0 0 0
## F3D5 0 0 8 0 2 0 0 0 0 9
## F3D6 0 0 0 0 5 0 0 25 0 9
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 0 16 11 5 0 0 0 0 0
## F3D9 0 0 9 13 6 0 0 0 0 19
## ASV148 ASV149 ASV150 ASV151 ASV152 ASV153 ASV154 ASV155 ASV156 ASV157
## F3D0 0 7 0 0 9 0 0 19 18 0
## F3D1 0 0 9 3 0 0 0 0 7 0
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 0 4 0 0 0 0 0 0 0 0
## F3D143 6 0 0 0 0 0 0 0 0 4
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 5 3 0 7 0 0 0 0 0
## F3D146 0 0 0 0 6 0 0 0 0 0
## F3D147 0 5 4 0 0 0 0 0 0 0
## F3D148 17 4 4 8 0 0 0 0 0 0
## F3D149 24 6 7 15 12 0 0 0 0 14
## F3D150 0 6 0 0 9 10 0 0 0 0
## F3D2 0 5 10 10 0 9 0 0 6 20
## F3D3 0 0 0 0 0 0 0 0 0 0
## F3D5 0 0 4 4 0 0 0 0 0 0
## F3D6 0 0 4 0 0 13 0 0 0 0
## F3D7 0 0 0 2 0 0 0 0 0 0
## F3D8 0 3 0 3 0 11 0 4 0 0
## F3D9 0 0 0 0 0 0 43 17 7 0
## ASV158 ASV159 ASV160 ASV161 ASV162 ASV163 ASV164 ASV165 ASV166 ASV167
## F3D0 0 0 21 10 0 0 0 0 0 11
## F3D1 0 0 0 6 0 0 0 0 0 0
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 4 0 0 0 0 0
## F3D146 21 0 0 11 0 0 0 0 0 0
## F3D147 0 0 0 0 6 0 0 13 11 0
## F3D148 0 0 10 0 15 0 0 0 5 0
## F3D149 0 0 4 0 9 0 0 6 0 0
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 17 37 0 8 0 20 0 0 8 0
## F3D3 0 0 0 0 0 0 12 10 0 0
## F3D5 0 0 0 0 0 0 0 3 0 0
## F3D6 0 0 0 0 0 4 0 0 0 7
## F3D7 0 0 0 0 0 0 5 0 0 0
## F3D8 0 0 0 0 0 0 8 0 0 3
## F3D9 0 0 0 0 0 10 9 0 8 10
## ASV168 ASV169 ASV170 ASV171 ASV172 ASV173 ASV174 ASV175 ASV176 ASV177
## F3D0 9 0 0 0 0 0 0 6 0 0
## F3D1 0 0 0 0 0 0 0 0 0 0
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 0 0 0 0 0
## F3D146 0 0 0 0 0 0 0 0 6 0
## F3D147 0 0 0 15 12 7 5 0 0 0
## F3D148 0 0 0 0 7 0 9 9 6 0
## F3D149 20 0 0 12 6 0 8 0 9 0
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 0 28 20 0 0 0 0 0 0 5
## F3D3 0 0 0 0 0 0 0 7 0 0
## F3D5 0 0 0 0 0 0 0 0 0 0
## F3D6 0 0 8 0 0 9 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 0 0 0 0 0 3 0 0 0
## F3D9 0 0 0 0 0 9 0 0 0 16
## ASV178 ASV179 ASV180 ASV181 ASV182 ASV183 ASV184 ASV185 ASV186 ASV187
## F3D0 3 0 0 5 0 10 3 0 0 0
## F3D1 0 11 0 0 0 0 0 0 0 0
## F3D141 0 0 0 3 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 5 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 0 3 0 0 0
## F3D146 0 0 0 0 0 0 0 0 0 0
## F3D147 0 0 8 0 0 0 11 0 0 0
## F3D148 0 0 0 4 0 0 0 0 0 0
## F3D149 5 0 0 6 0 0 0 0 0 0
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 3 0 6 0 0 7 0 0 0 7
## F3D3 0 0 0 0 0 0 0 0 0 0
## F3D5 0 0 0 0 0 0 0 0 0 0
## F3D6 9 0 0 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 9 0 0 0 0 0 12 0 0
## F3D9 0 0 5 0 18 0 0 0 17 9
## ASV188 ASV189 ASV190 ASV191 ASV192 ASV193 ASV194 ASV195 ASV196 ASV197
## F3D0 0 0 0 0 0 0 0 12 0 0
## F3D1 0 3 0 0 0 0 0 0 0 0
## F3D141 0 0 5 0 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 9 0 0 0 0 0 0 0
## F3D145 0 0 0 8 0 0 0 0 0 0
## F3D146 0 3 0 6 0 0 0 0 0 0
## F3D147 0 0 0 0 14 0 0 0 0 0
## F3D148 0 0 0 0 0 0 0 0 0 0
## F3D149 0 0 0 0 0 0 0 0 0 0
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 0 0 0 0 0 10 13 0 12 5
## F3D3 0 0 0 0 0 0 0 0 0 0
## F3D5 0 0 0 0 0 0 0 0 0 0
## F3D6 0 0 0 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 3 0 0 0 4 0 0 0 0
## F3D9 0 5 0 0 0 0 0 0 0 6
## ASV198 ASV199 ASV200 ASV201 ASV202 ASV203 ASV204 ASV205 ASV206 ASV207
## F3D0 10 5 0 0 0 0 0 0 0 0
## F3D1 0 5 0 0 0 0 0 8 0 0
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 0 0 5 0 0 0 0 0 2 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 0 0 0 0 0
## F3D146 0 0 0 2 0 0 0 0 0 0
## F3D147 0 0 0 3 0 0 0 0 4 0
## F3D148 0 0 5 0 0 0 0 0 2 0
## F3D149 0 0 0 2 0 0 0 0 0 8
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 0 0 0 0 9 0 0 0 0 0
## F3D3 0 0 0 0 0 0 0 0 0 0
## F3D5 0 0 0 0 0 0 0 0 0 0
## F3D6 0 0 0 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 0 0 0 0 3 0 0 0 0
## F3D9 0 0 0 3 0 6 9 0 0 0
## ASV208 ASV209 ASV210 ASV211 ASV212 ASV213 ASV214 ASV215 ASV216 ASV217
## F3D0 0 0 0 0 0 0 0 0 0 4
## F3D1 0 0 0 0 0 0 0 0 0 0
## F3D141 0 0 0 0 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 0 0 0 0 0
## F3D146 0 0 0 0 0 0 0 0 0 0
## F3D147 0 0 0 0 0 6 0 0 0 0
## F3D148 0 0 7 0 0 0 0 0 0 0
## F3D149 8 0 0 0 0 0 0 0 5 0
## F3D150 0 0 0 0 0 0 0 0 0 0
## F3D2 0 0 0 0 0 0 6 6 0 0
## F3D3 0 0 0 7 0 0 0 0 0 0
## F3D5 0 0 0 0 0 0 0 0 0 0
## F3D6 0 0 0 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0 0 0
## F3D8 0 0 0 0 7 0 0 0 0 0
## F3D9 0 8 0 0 0 0 0 0 0 0
## ASV218 ASV219 ASV220 ASV221 ASV222 ASV223 ASV224 ASV225
## F3D0 4 0 0 0 0 0 0 0
## F3D1 0 0 0 0 0 0 0 0
## F3D141 0 4 0 0 0 0 0 0
## F3D142 0 0 0 0 0 0 0 0
## F3D143 0 0 0 0 0 0 0 0
## F3D144 0 0 0 0 0 0 0 0
## F3D145 0 0 0 0 0 0 0 0
## F3D146 0 0 0 0 0 0 0 0
## F3D147 0 0 0 0 0 0 3 0
## F3D148 0 0 0 0 0 0 0 0
## F3D149 0 0 0 0 0 0 0 0
## F3D150 0 0 0 0 0 0 0 0
## F3D2 0 0 4 4 0 0 0 0
## F3D3 0 0 0 0 4 0 0 2
## F3D5 0 0 0 0 0 0 0 0
## F3D6 0 0 0 0 0 0 0 0
## F3D7 0 0 0 0 0 0 0 0
## F3D8 0 0 0 0 0 0 0 0
## F3D9 0 0 0 0 0 4 0 0Tax table
tax_table object? function tax_table(). It
contains information about taxonomic rank of the ASVs.
tax_table(phyloseq)## Taxonomy Table: [225 taxa by 6 taxonomic ranks]:
## Kingdom Phylum Class
## ASV1 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV2 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV3 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV4 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV5 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV6 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV7 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV8 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV9 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV10 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV11 "Bacteria" "Firmicutes" "Bacilli"
## ASV12 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV13 "Bacteria" "Firmicutes" "Bacilli"
## ASV14 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV15 "Bacteria" "Firmicutes" "Clostridia"
## ASV16 "Bacteria" "Firmicutes" "Bacilli"
## ASV17 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV18 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV19 "Bacteria" "Firmicutes" "Bacilli"
## ASV20 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV21 "Bacteria" "Firmicutes" "Bacilli"
## ASV22 "Bacteria" "Firmicutes" "Clostridia"
## ASV23 "Bacteria" "Firmicutes" "Clostridia"
## ASV24 "Bacteria" "Firmicutes" "Clostridia"
## ASV25 "Bacteria" "Firmicutes" "Clostridia"
## ASV26 "Bacteria" "Firmicutes" "Clostridia"
## ASV27 "Bacteria" "Firmicutes" "Clostridia"
## ASV28 "Bacteria" "Firmicutes" "Clostridia"
## ASV29 "Bacteria" "Firmicutes" "Clostridia"
## ASV30 "Bacteria" "Firmicutes" "Clostridia"
## ASV31 "Bacteria" "Firmicutes" "Clostridia"
## ASV32 "Bacteria" "Firmicutes" "Clostridia"
## ASV33 "Bacteria" "Firmicutes" "Clostridia"
## ASV34 "Bacteria" "Firmicutes" "Bacilli"
## ASV35 "Bacteria" "Firmicutes" "Clostridia"
## ASV36 "Bacteria" "Firmicutes" "Clostridia"
## ASV37 "Bacteria" "Firmicutes" "Clostridia"
## ASV38 "Bacteria" "Firmicutes" "Clostridia"
## ASV39 "Bacteria" "Firmicutes" "Clostridia"
## ASV40 "Bacteria" "Firmicutes" "Clostridia"
## ASV41 "Bacteria" "Firmicutes" "Clostridia"
## ASV42 "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV43 "Bacteria" "Firmicutes" "Clostridia"
## ASV44 "Bacteria" "Firmicutes" "Clostridia"
## ASV45 "Bacteria" "Firmicutes" "Bacilli"
## ASV46 "Bacteria" "Firmicutes" "Clostridia"
## ASV47 "Bacteria" "Firmicutes" "Clostridia"
## ASV48 "Bacteria" "Firmicutes" "Clostridia"
## ASV49 "Bacteria" "Firmicutes" "Clostridia"
## ASV50 "Bacteria" "Firmicutes" "Clostridia"
## ASV51 "Bacteria" "Campylobacterota" "Campylobacteria"
## ASV52 "Bacteria" "Firmicutes" "Clostridia"
## ASV53 "Bacteria" "Firmicutes" "Clostridia"
## ASV54 "Bacteria" "Firmicutes" "Clostridia"
## ASV55 "Bacteria" "Firmicutes" "Clostridia"
## ASV56 "Bacteria" "Firmicutes" "Clostridia"
## ASV57 "Bacteria" "Firmicutes" "Clostridia"
## ASV58 "Bacteria" "Firmicutes" "Clostridia"
## ASV59 "Bacteria" "Firmicutes" "Bacilli"
## ASV60 "Bacteria" "Actinobacteriota" "Actinobacteria"
## ASV61 "Bacteria" "Firmicutes" "Bacilli"
## ASV62 "Bacteria" "Firmicutes" "Clostridia"
## ASV63 "Bacteria" "Firmicutes" "Clostridia"
## ASV64 "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV65 "Bacteria" "Firmicutes" "Clostridia"
## ASV66 "Bacteria" "Firmicutes" "Clostridia"
## ASV67 "Bacteria" "Actinobacteriota" "Actinobacteria"
## ASV68 "Bacteria" "Firmicutes" "Clostridia"
## ASV69 "Bacteria" "Firmicutes" "Clostridia"
## ASV70 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV71 "Bacteria" "Firmicutes" "Clostridia"
## ASV72 "Bacteria" "Firmicutes" "Clostridia"
## ASV73 "Bacteria" "Firmicutes" "Clostridia"
## ASV74 "Bacteria" "Firmicutes" "Clostridia"
## ASV75 "Bacteria" "Firmicutes" "Clostridia"
## ASV76 "Bacteria" "Firmicutes" "Clostridia"
## ASV77 "Bacteria" "Firmicutes" "Clostridia"
## ASV78 "Bacteria" "Firmicutes" "Clostridia"
## ASV79 "Bacteria" "Firmicutes" "Clostridia"
## ASV80 "Bacteria" "Firmicutes" "Clostridia"
## ASV81 "Bacteria" "Firmicutes" "Clostridia"
## ASV82 "Bacteria" "Firmicutes" "Clostridia"
## ASV83 "Bacteria" "Firmicutes" "Bacilli"
## ASV84 "Bacteria" "Firmicutes" "Clostridia"
## ASV85 "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV86 "Bacteria" "Firmicutes" "Clostridia"
## ASV87 "Bacteria" "Firmicutes" "Clostridia"
## ASV88 "Bacteria" "Firmicutes" "Clostridia"
## ASV89 "Bacteria" "Firmicutes" "Clostridia"
## ASV90 "Bacteria" "Firmicutes" "Clostridia"
## ASV91 "Bacteria" "Firmicutes" "Bacilli"
## ASV92 "Bacteria" "Firmicutes" "Clostridia"
## ASV93 "Bacteria" "Firmicutes" "Clostridia"
## ASV94 "Bacteria" "Patescibacteria" "Saccharimonadia"
## ASV95 "Bacteria" "Firmicutes" "Clostridia"
## ASV96 "Bacteria" "Firmicutes" "Clostridia"
## ASV97 "Bacteria" "Firmicutes" "Clostridia"
## ASV98 "Bacteria" "Firmicutes" "Bacilli"
## ASV99 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV100 "Bacteria" "Firmicutes" "Clostridia"
## ASV101 "Bacteria" "Firmicutes" "Clostridia"
## ASV102 "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV103 "Bacteria" "Firmicutes" "Bacilli"
## ASV104 "Bacteria" "Firmicutes" "Clostridia"
## ASV105 "Bacteria" "Firmicutes" "Clostridia"
## ASV106 "Bacteria" "Proteobacteria" "Alphaproteobacteria"
## ASV107 "Bacteria" "Deinococcota" "Deinococci"
## ASV108 "Bacteria" "Firmicutes" "Clostridia"
## ASV109 "Bacteria" "Firmicutes" "Clostridia"
## ASV110 "Bacteria" "Firmicutes" "Clostridia"
## ASV111 "Bacteria" "Firmicutes" "Clostridia"
## ASV112 "Bacteria" "Firmicutes" "Clostridia"
## ASV113 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV114 "Bacteria" "Firmicutes" "Clostridia"
## ASV115 "Bacteria" "Firmicutes" "Clostridia"
## ASV116 "Bacteria" "Firmicutes" "Clostridia"
## ASV117 "Bacteria" "Firmicutes" "Clostridia"
## ASV118 "Bacteria" "Firmicutes" "Clostridia"
## ASV119 "Bacteria" "Firmicutes" "Clostridia"
## ASV120 "Bacteria" "Firmicutes" "Clostridia"
## ASV121 "Bacteria" "Firmicutes" "Clostridia"
## ASV122 "Bacteria" "Firmicutes" "Clostridia"
## ASV123 "Bacteria" "Firmicutes" "Clostridia"
## ASV124 "Bacteria" "Firmicutes" "Clostridia"
## ASV125 "Bacteria" "Firmicutes" "Clostridia"
## ASV126 "Bacteria" "Firmicutes" "Clostridia"
## ASV127 "Bacteria" "Firmicutes" "Clostridia"
## ASV128 "Bacteria" "Firmicutes" "Clostridia"
## ASV129 "Bacteria" "Firmicutes" "Clostridia"
## ASV130 "Bacteria" "Firmicutes" "Clostridia"
## ASV131 "Bacteria" "Firmicutes" "Clostridia"
## ASV132 "Bacteria" "Firmicutes" "Clostridia"
## ASV133 "Bacteria" "Firmicutes" "Clostridia"
## ASV134 "Bacteria" "Firmicutes" "Clostridia"
## ASV135 "Bacteria" "Firmicutes" "Clostridia"
## ASV136 "Bacteria" "Firmicutes" "Clostridia"
## ASV137 "Bacteria" "Firmicutes" "Clostridia"
## ASV138 "Bacteria" "Firmicutes" "Bacilli"
## ASV139 "Bacteria" "Bacteroidota" "Bacteroidia"
## ASV140 "Bacteria" "Firmicutes" "Clostridia"
## ASV141 "Bacteria" "Firmicutes" "Clostridia"
## ASV142 "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV143 "Bacteria" "Firmicutes" "Clostridia"
## ASV144 "Bacteria" "Proteobacteria" "Alphaproteobacteria"
## ASV145 "Bacteria" "Firmicutes" "Clostridia"
## ASV146 "Bacteria" "Firmicutes" "Clostridia"
## ASV147 "Bacteria" "Firmicutes" "Clostridia"
## ASV148 "Bacteria" "Firmicutes" "Clostridia"
## ASV149 "Bacteria" "Firmicutes" "Clostridia"
## ASV150 "Bacteria" "Firmicutes" "Clostridia"
## ASV151 "Bacteria" "Actinobacteriota" "Coriobacteriia"
## ASV152 "Bacteria" "Firmicutes" "Clostridia"
## ASV153 "Bacteria" "Firmicutes" "Clostridia"
## ASV154 "Bacteria" "Firmicutes" "Clostridia"
## ASV155 "Bacteria" "Firmicutes" "Clostridia"
## ASV156 "Bacteria" "Firmicutes" "Clostridia"
## ASV157 "Bacteria" "Firmicutes" "Clostridia"
## ASV158 "Bacteria" "Firmicutes" "Clostridia"
## ASV159 "Bacteria" "Firmicutes" "Clostridia"
## ASV160 "Bacteria" "Firmicutes" "Clostridia"
## ASV161 "Bacteria" "Firmicutes" "Clostridia"
## ASV162 "Bacteria" "Firmicutes" "Clostridia"
## ASV163 "Bacteria" "Firmicutes" "Clostridia"
## ASV164 "Bacteria" "Firmicutes" "Clostridia"
## ASV165 "Bacteria" "Firmicutes" "Clostridia"
## ASV166 "Bacteria" "Firmicutes" "Clostridia"
## ASV167 "Bacteria" "Firmicutes" "Clostridia"
## ASV168 "Bacteria" "Firmicutes" "Clostridia"
## ASV169 "Bacteria" "Firmicutes" "Clostridia"
## ASV170 "Bacteria" "Firmicutes" "Clostridia"
## ASV171 "Bacteria" "Firmicutes" "Clostridia"
## ASV172 "Bacteria" "Firmicutes" "Clostridia"
## ASV173 "Bacteria" "Firmicutes" "Clostridia"
## ASV174 "Bacteria" "Firmicutes" "Clostridia"
## ASV175 "Bacteria" "Firmicutes" "Clostridia"
## ASV176 "Bacteria" "Firmicutes" "Clostridia"
## ASV177 "Bacteria" "Firmicutes" "Clostridia"
## ASV178 "Bacteria" "Firmicutes" "Clostridia"
## ASV179 "Bacteria" "Firmicutes" "Clostridia"
## ASV180 "Bacteria" "Firmicutes" "Clostridia"
## ASV181 "Bacteria" "Firmicutes" "Clostridia"
## ASV182 "Bacteria" "Firmicutes" "Clostridia"
## ASV183 "Bacteria" "Verrucomicrobiota" "Verrucomicrobiae"
## ASV184 "Bacteria" "Actinobacteriota" "Coriobacteriia"
## ASV185 "Bacteria" "Cyanobacteria" "Cyanobacteriia"
## ASV186 "Bacteria" "Firmicutes" "Clostridia"
## ASV187 "Bacteria" "Firmicutes" "Clostridia"
## ASV188 "Bacteria" "Firmicutes" "Bacilli"
## ASV189 "Bacteria" "Firmicutes" "Clostridia"
## ASV190 "Bacteria" "Patescibacteria" "Saccharimonadia"
## ASV191 "Bacteria" "Firmicutes" "Clostridia"
## ASV192 "Bacteria" "Firmicutes" "Clostridia"
## ASV193 "Bacteria" "Firmicutes" "Clostridia"
## ASV194 "Bacteria" "Firmicutes" "Clostridia"
## ASV195 "Bacteria" "Firmicutes" "Clostridia"
## ASV196 "Bacteria" "Firmicutes" "Clostridia"
## ASV197 "Bacteria" "Cyanobacteria" "Cyanobacteriia"
## ASV198 "Bacteria" "Firmicutes" "Clostridia"
## ASV199 "Bacteria" "Firmicutes" "Bacilli"
## ASV200 "Bacteria" "Firmicutes" "Clostridia"
## ASV201 "Bacteria" "Actinobacteriota" "Coriobacteriia"
## ASV202 "Bacteria" "Firmicutes" "Clostridia"
## ASV203 "Bacteria" "Firmicutes" "Clostridia"
## ASV204 "Bacteria" "Firmicutes" "Clostridia"
## ASV205 "Bacteria" "Firmicutes" "Clostridia"
## ASV206 "Bacteria" "Firmicutes" "Bacilli"
## ASV207 "Bacteria" "Firmicutes" "Clostridia"
## ASV208 "Bacteria" "Firmicutes" "Clostridia"
## ASV209 "Bacteria" "Firmicutes" "Clostridia"
## ASV210 "Bacteria" "Firmicutes" "Clostridia"
## ASV211 "Bacteria" "Firmicutes" "Bacilli"
## ASV212 "Bacteria" "Firmicutes" "Clostridia"
## ASV213 "Bacteria" "Firmicutes" "Clostridia"
## ASV214 "Bacteria" "Firmicutes" "Clostridia"
## ASV215 "Bacteria" "Firmicutes" "Bacilli"
## ASV216 "Bacteria" "Firmicutes" "Clostridia"
## ASV217 "Bacteria" "Firmicutes" "Clostridia"
## ASV218 "Bacteria" "Firmicutes" "Clostridia"
## ASV219 "Bacteria" "Firmicutes" "Clostridia"
## ASV220 "Bacteria" "Firmicutes" "Clostridia"
## ASV221 "Bacteria" "Firmicutes" "Clostridia"
## ASV222 "Bacteria" "Cyanobacteria" "Cyanobacteriia"
## ASV223 "Bacteria" "Firmicutes" "Clostridia"
## ASV224 "Bacteria" "Actinobacteriota" "Coriobacteriia"
## ASV225 "Bacteria" "Firmicutes" "Bacilli"
## Order
## ASV1 "Bacteroidales"
## ASV2 "Bacteroidales"
## ASV3 "Bacteroidales"
## ASV4 "Bacteroidales"
## ASV5 "Bacteroidales"
## ASV6 "Bacteroidales"
## ASV7 "Bacteroidales"
## ASV8 "Bacteroidales"
## ASV9 "Bacteroidales"
## ASV10 "Bacteroidales"
## ASV11 "Lactobacillales"
## ASV12 "Bacteroidales"
## ASV13 "Lactobacillales"
## ASV14 "Bacteroidales"
## ASV15 "Lachnospirales"
## ASV16 "Erysipelotrichales"
## ASV17 "Bacteroidales"
## ASV18 "Bacteroidales"
## ASV19 "RF39"
## ASV20 "Bacteroidales"
## ASV21 "Lactobacillales"
## ASV22 "Lachnospirales"
## ASV23 "Lachnospirales"
## ASV24 "Peptococcales"
## ASV25 "Lachnospirales"
## ASV26 "Oscillospirales"
## ASV27 "Oscillospirales"
## ASV28 "Lachnospirales"
## ASV29 "Lachnospirales"
## ASV30 "Lachnospirales"
## ASV31 "Lachnospirales"
## ASV32 "Lachnospirales"
## ASV33 "Lachnospirales"
## ASV34 "Staphylococcales"
## ASV35 "Lachnospirales"
## ASV36 "Lachnospirales"
## ASV37 "Lachnospirales"
## ASV38 "Lachnospirales"
## ASV39 "Lachnospirales"
## ASV40 "Lachnospirales"
## ASV41 "Lachnospirales"
## ASV42 "Pseudomonadales"
## ASV43 "Lachnospirales"
## ASV44 "Lachnospirales"
## ASV45 "Bacillales"
## ASV46 "Lachnospirales"
## ASV47 "Lachnospirales"
## ASV48 "Lachnospirales"
## ASV49 "Lachnospirales"
## ASV50 "Oscillospirales"
## ASV51 "Campylobacterales"
## ASV52 "Lachnospirales"
## ASV53 "Peptostreptococcales-Tissierellales"
## ASV54 "Lachnospirales"
## ASV55 "Lachnospirales"
## ASV56 "Oscillospirales"
## ASV57 "Lachnospirales"
## ASV58 "Lachnospirales"
## ASV59 "Acholeplasmatales"
## ASV60 "Actinomycetales"
## ASV61 "RF39"
## ASV62 "Oscillospirales"
## ASV63 "Clostridiales"
## ASV64 "Burkholderiales"
## ASV65 "Oscillospirales"
## ASV66 "Lachnospirales"
## ASV67 "Bifidobacteriales"
## ASV68 "Lachnospirales"
## ASV69 "Lachnospirales"
## ASV70 "Bacteroidales"
## ASV71 "Lachnospirales"
## ASV72 "Lachnospirales"
## ASV73 "Lachnospirales"
## ASV74 "Lachnospirales"
## ASV75 "Clostridiales"
## ASV76 "Lachnospirales"
## ASV77 "Lachnospirales"
## ASV78 "Lachnospirales"
## ASV79 "Oscillospirales"
## ASV80 "Clostridia vadinBB60 group"
## ASV81 "Oscillospirales"
## ASV82 "Lachnospirales"
## ASV83 "Lactobacillales"
## ASV84 "Lachnospirales"
## ASV85 "Enterobacterales"
## ASV86 "Lachnospirales"
## ASV87 "Lachnospirales"
## ASV88 "Lachnospirales"
## ASV89 "Lachnospirales"
## ASV90 "Lachnospirales"
## ASV91 "Lactobacillales"
## ASV92 "Oscillospirales"
## ASV93 "Oscillospirales"
## ASV94 "Saccharimonadales"
## ASV95 "Lachnospirales"
## ASV96 "Lachnospirales"
## ASV97 "Lachnospirales"
## ASV98 "Lactobacillales"
## ASV99 "Bacteroidales"
## ASV100 "Lachnospirales"
## ASV101 "Peptococcales"
## ASV102 "Pseudomonadales"
## ASV103 "Lactobacillales"
## ASV104 "Lachnospirales"
## ASV105 "Lachnospirales"
## ASV106 "Rickettsiales"
## ASV107 "Deinococcales"
## ASV108 "Clostridia vadinBB60 group"
## ASV109 "Lachnospirales"
## ASV110 "Oscillospirales"
## ASV111 "Lachnospirales"
## ASV112 "Lachnospirales"
## ASV113 "Bacteroidales"
## ASV114 "Oscillospirales"
## ASV115 "Clostridia UCG-014"
## ASV116 "Lachnospirales"
## ASV117 "Lachnospirales"
## ASV118 "Lachnospirales"
## ASV119 "Lachnospirales"
## ASV120 "Lachnospirales"
## ASV121 "Lachnospirales"
## ASV122 "Lachnospirales"
## ASV123 "Lachnospirales"
## ASV124 "Lachnospirales"
## ASV125 "Lachnospirales"
## ASV126 "Lachnospirales"
## ASV127 "Lachnospirales"
## ASV128 "Lachnospirales"
## ASV129 "Lachnospirales"
## ASV130 "Lachnospirales"
## ASV131 "Lachnospirales"
## ASV132 "Lachnospirales"
## ASV133 "Oscillospirales"
## ASV134 "Lachnospirales"
## ASV135 "Lachnospirales"
## ASV136 "Lachnospirales"
## ASV137 "Lachnospirales"
## ASV138 "RF39"
## ASV139 "Bacteroidales"
## ASV140 "Lachnospirales"
## ASV141 "Lachnospirales"
## ASV142 "Pseudomonadales"
## ASV143 "Lachnospirales"
## ASV144 "Rhodobacterales"
## ASV145 "Lachnospirales"
## ASV146 "Lachnospirales"
## ASV147 "Lachnospirales"
## ASV148 "Lachnospirales"
## ASV149 "Christensenellales"
## ASV150 "Peptostreptococcales-Tissierellales"
## ASV151 "Coriobacteriales"
## ASV152 "Lachnospirales"
## ASV153 "Lachnospirales"
## ASV154 "Lachnospirales"
## ASV155 "Clostridia vadinBB60 group"
## ASV156 "Clostridia vadinBB60 group"
## ASV157 "Lachnospirales"
## ASV158 "Lachnospirales"
## ASV159 "Lachnospirales"
## ASV160 "Oscillospirales"
## ASV161 "Oscillospirales"
## ASV162 "Lachnospirales"
## ASV163 "Lachnospirales"
## ASV164 "Lachnospirales"
## ASV165 "Clostridia UCG-014"
## ASV166 "Lachnospirales"
## ASV167 "Lachnospirales"
## ASV168 "Lachnospirales"
## ASV169 "Oscillospirales"
## ASV170 "Oscillospirales"
## ASV171 "Lachnospirales"
## ASV172 "Lachnospirales"
## ASV173 "Lachnospirales"
## ASV174 "Lachnospirales"
## ASV175 "Oscillospirales"
## ASV176 "Lachnospirales"
## ASV177 "Lachnospirales"
## ASV178 "Oscillospirales"
## ASV179 "Lachnospirales"
## ASV180 "Lachnospirales"
## ASV181 "Oscillospirales"
## ASV182 "Lachnospirales"
## ASV183 "Verrucomicrobiales"
## ASV184 "Coriobacteriales"
## ASV185 "Chloroplast"
## ASV186 "Lachnospirales"
## ASV187 "Oscillospirales"
## ASV188 "Lactobacillales"
## ASV189 "Lachnospirales"
## ASV190 "Saccharimonadales"
## ASV191 "Lachnospirales"
## ASV192 "Clostridia UCG-014"
## ASV193 "Lachnospirales"
## ASV194 "Oscillospirales"
## ASV195 "Oscillospirales"
## ASV196 "Lachnospirales"
## ASV197 "Chloroplast"
## ASV198 "Clostridia vadinBB60 group"
## ASV199 "Lactobacillales"
## ASV200 "Clostridiales"
## ASV201 "Coriobacteriales"
## ASV202 "Lachnospirales"
## ASV203 "Lachnospirales"
## ASV204 "Lachnospirales"
## ASV205 "Lachnospirales"
## ASV206 "Erysipelotrichales"
## ASV207 "Lachnospirales"
## ASV208 "Lachnospirales"
## ASV209 "Clostridia UCG-014"
## ASV210 "Lachnospirales"
## ASV211 "Lactobacillales"
## ASV212 "Oscillospirales"
## ASV213 "Oscillospirales"
## ASV214 "Oscillospirales"
## ASV215 "Lactobacillales"
## ASV216 "Lachnospirales"
## ASV217 "Lachnospirales"
## ASV218 "Clostridia vadinBB60 group"
## ASV219 "Clostridia UCG-014"
## ASV220 "Lachnospirales"
## ASV221 "Clostridia vadinBB60 group"
## ASV222 "Chloroplast"
## ASV223 "Clostridia UCG-014"
## ASV224 "Coriobacteriales"
## ASV225 "RF39"
## Family
## ASV1 "Muribaculaceae"
## ASV2 "Muribaculaceae"
## ASV3 "Muribaculaceae"
## ASV4 "Muribaculaceae"
## ASV5 "Bacteroidaceae"
## ASV6 "Muribaculaceae"
## ASV7 "Muribaculaceae"
## ASV8 "Rikenellaceae"
## ASV9 "Muribaculaceae"
## ASV10 "Muribaculaceae"
## ASV11 "Lactobacillaceae"
## ASV12 "Muribaculaceae"
## ASV13 "Lactobacillaceae"
## ASV14 "Muribaculaceae"
## ASV15 "Lachnospiraceae"
## ASV16 "Erysipelotrichaceae"
## ASV17 "Muribaculaceae"
## ASV18 "Muribaculaceae"
## ASV19 NA
## ASV20 "Muribaculaceae"
## ASV21 "Lactobacillaceae"
## ASV22 "Lachnospiraceae"
## ASV23 "Lachnospiraceae"
## ASV24 "Peptococcaceae"
## ASV25 "Lachnospiraceae"
## ASV26 "Oscillospiraceae"
## ASV27 "Oscillospiraceae"
## ASV28 "Lachnospiraceae"
## ASV29 "Lachnospiraceae"
## ASV30 "Lachnospiraceae"
## ASV31 "Lachnospiraceae"
## ASV32 "Lachnospiraceae"
## ASV33 "Lachnospiraceae"
## ASV34 "Staphylococcaceae"
## ASV35 "Lachnospiraceae"
## ASV36 "Lachnospiraceae"
## ASV37 "Lachnospiraceae"
## ASV38 "Lachnospiraceae"
## ASV39 "Lachnospiraceae"
## ASV40 "Lachnospiraceae"
## ASV41 "Lachnospiraceae"
## ASV42 "Moraxellaceae"
## ASV43 "Lachnospiraceae"
## ASV44 "Lachnospiraceae"
## ASV45 "Bacillaceae"
## ASV46 "Lachnospiraceae"
## ASV47 "Lachnospiraceae"
## ASV48 "Lachnospiraceae"
## ASV49 "Lachnospiraceae"
## ASV50 "Ruminococcaceae"
## ASV51 "Helicobacteraceae"
## ASV52 "Lachnospiraceae"
## ASV53 "Anaerovoracaceae"
## ASV54 "Lachnospiraceae"
## ASV55 "Lachnospiraceae"
## ASV56 "Ruminococcaceae"
## ASV57 "Lachnospiraceae"
## ASV58 "Lachnospiraceae"
## ASV59 "Acholeplasmataceae"
## ASV60 "Actinomycetaceae"
## ASV61 NA
## ASV62 "Oscillospiraceae"
## ASV63 "Clostridiaceae"
## ASV64 "Neisseriaceae"
## ASV65 "Oscillospiraceae"
## ASV66 "Lachnospiraceae"
## ASV67 "Bifidobacteriaceae"
## ASV68 "Lachnospiraceae"
## ASV69 "Lachnospiraceae"
## ASV70 "Bacteroidaceae"
## ASV71 "Lachnospiraceae"
## ASV72 "Lachnospiraceae"
## ASV73 "Lachnospiraceae"
## ASV74 "Lachnospiraceae"
## ASV75 "Clostridiaceae"
## ASV76 "Lachnospiraceae"
## ASV77 "Lachnospiraceae"
## ASV78 "Lachnospiraceae"
## ASV79 "Oscillospiraceae"
## ASV80 NA
## ASV81 "Oscillospiraceae"
## ASV82 "Lachnospiraceae"
## ASV83 "Streptococcaceae"
## ASV84 "Lachnospiraceae"
## ASV85 "Enterobacteriaceae"
## ASV86 "Lachnospiraceae"
## ASV87 "Lachnospiraceae"
## ASV88 "Lachnospiraceae"
## ASV89 "Lachnospiraceae"
## ASV90 "Lachnospiraceae"
## ASV91 "Enterococcaceae"
## ASV92 "Oscillospiraceae"
## ASV93 "Oscillospiraceae"
## ASV94 "Saccharimonadaceae"
## ASV95 "Lachnospiraceae"
## ASV96 "Lachnospiraceae"
## ASV97 "Lachnospiraceae"
## ASV98 "Listeriaceae"
## ASV99 "Muribaculaceae"
## ASV100 "Lachnospiraceae"
## ASV101 "Peptococcaceae"
## ASV102 "Pseudomonadaceae"
## ASV103 "Streptococcaceae"
## ASV104 "Lachnospiraceae"
## ASV105 "Lachnospiraceae"
## ASV106 "Mitochondria"
## ASV107 "Deinococcaceae"
## ASV108 NA
## ASV109 "Lachnospiraceae"
## ASV110 "Ruminococcaceae"
## ASV111 "Lachnospiraceae"
## ASV112 "Lachnospiraceae"
## ASV113 "Porphyromonadaceae"
## ASV114 "Oscillospiraceae"
## ASV115 NA
## ASV116 "Lachnospiraceae"
## ASV117 "Lachnospiraceae"
## ASV118 "Lachnospiraceae"
## ASV119 "Lachnospiraceae"
## ASV120 "Lachnospiraceae"
## ASV121 "Lachnospiraceae"
## ASV122 "Lachnospiraceae"
## ASV123 "Lachnospiraceae"
## ASV124 "Lachnospiraceae"
## ASV125 "Lachnospiraceae"
## ASV126 "Lachnospiraceae"
## ASV127 "Lachnospiraceae"
## ASV128 "Lachnospiraceae"
## ASV129 "Lachnospiraceae"
## ASV130 "Lachnospiraceae"
## ASV131 "Lachnospiraceae"
## ASV132 "Lachnospiraceae"
## ASV133 "Oscillospiraceae"
## ASV134 "Lachnospiraceae"
## ASV135 "Lachnospiraceae"
## ASV136 "Lachnospiraceae"
## ASV137 "Lachnospiraceae"
## ASV138 NA
## ASV139 "Muribaculaceae"
## ASV140 "Lachnospiraceae"
## ASV141 "Lachnospiraceae"
## ASV142 "Pseudomonadaceae"
## ASV143 "Lachnospiraceae"
## ASV144 "Rhodobacteraceae"
## ASV145 "Lachnospiraceae"
## ASV146 "Lachnospiraceae"
## ASV147 "Lachnospiraceae"
## ASV148 "Lachnospiraceae"
## ASV149 "Christensenellaceae"
## ASV150 "Anaerovoracaceae"
## ASV151 "Eggerthellaceae"
## ASV152 "Lachnospiraceae"
## ASV153 "Lachnospiraceae"
## ASV154 "Lachnospiraceae"
## ASV155 NA
## ASV156 NA
## ASV157 "Lachnospiraceae"
## ASV158 "Lachnospiraceae"
## ASV159 "Lachnospiraceae"
## ASV160 "[Eubacterium] coprostanoligenes group"
## ASV161 "Oscillospiraceae"
## ASV162 "Lachnospiraceae"
## ASV163 "Lachnospiraceae"
## ASV164 "Lachnospiraceae"
## ASV165 NA
## ASV166 "Lachnospiraceae"
## ASV167 "Lachnospiraceae"
## ASV168 "Lachnospiraceae"
## ASV169 "Ruminococcaceae"
## ASV170 "Oscillospiraceae"
## ASV171 "Lachnospiraceae"
## ASV172 "Lachnospiraceae"
## ASV173 "Lachnospiraceae"
## ASV174 "Lachnospiraceae"
## ASV175 "Oscillospiraceae"
## ASV176 "Lachnospiraceae"
## ASV177 "Lachnospiraceae"
## ASV178 "Ruminococcaceae"
## ASV179 "Lachnospiraceae"
## ASV180 "Lachnospiraceae"
## ASV181 "Ruminococcaceae"
## ASV182 "Lachnospiraceae"
## ASV183 "Akkermansiaceae"
## ASV184 "Eggerthellaceae"
## ASV185 NA
## ASV186 "Lachnospiraceae"
## ASV187 "Butyricicoccaceae"
## ASV188 "Streptococcaceae"
## ASV189 "Lachnospiraceae"
## ASV190 "Saccharimonadaceae"
## ASV191 "Lachnospiraceae"
## ASV192 NA
## ASV193 "Lachnospiraceae"
## ASV194 "Ruminococcaceae"
## ASV195 "Ruminococcaceae"
## ASV196 "Lachnospiraceae"
## ASV197 NA
## ASV198 NA
## ASV199 "Streptococcaceae"
## ASV200 "Clostridiaceae"
## ASV201 "Eggerthellaceae"
## ASV202 "Lachnospiraceae"
## ASV203 "Lachnospiraceae"
## ASV204 "Lachnospiraceae"
## ASV205 "Lachnospiraceae"
## ASV206 "Erysipelatoclostridiaceae"
## ASV207 "Lachnospiraceae"
## ASV208 "Lachnospiraceae"
## ASV209 NA
## ASV210 "Lachnospiraceae"
## ASV211 "Streptococcaceae"
## ASV212 "Ruminococcaceae"
## ASV213 "Oscillospiraceae"
## ASV214 "Oscillospiraceae"
## ASV215 "Streptococcaceae"
## ASV216 "Lachnospiraceae"
## ASV217 "Lachnospiraceae"
## ASV218 NA
## ASV219 NA
## ASV220 "Lachnospiraceae"
## ASV221 NA
## ASV222 NA
## ASV223 NA
## ASV224 "Atopobiaceae"
## ASV225 NA
## Genus
## ASV1 NA
## ASV2 NA
## ASV3 NA
## ASV4 NA
## ASV5 "Bacteroides"
## ASV6 NA
## ASV7 NA
## ASV8 "Alistipes"
## ASV9 NA
## ASV10 NA
## ASV11 "Lactobacillus"
## ASV12 NA
## ASV13 "Ligilactobacillus"
## ASV14 NA
## ASV15 "Lachnospiraceae NK4A136 group"
## ASV16 "Turicibacter"
## ASV17 NA
## ASV18 NA
## ASV19 NA
## ASV20 NA
## ASV21 "HT002"
## ASV22 NA
## ASV23 "Lachnospiraceae NK4A136 group"
## ASV24 NA
## ASV25 NA
## ASV26 "Oscillibacter"
## ASV27 "Oscillibacter"
## ASV28 "Lachnospiraceae NK4A136 group"
## ASV29 "Lachnospiraceae NK4A136 group"
## ASV30 NA
## ASV31 "Lachnospiraceae NK4A136 group"
## ASV32 NA
## ASV33 "Lachnospiraceae NK4A136 group"
## ASV34 "Staphylococcus"
## ASV35 NA
## ASV36 "Lachnospiraceae NK4A136 group"
## ASV37 "Lachnospiraceae NK4A136 group"
## ASV38 "Lachnospiraceae NK4A136 group"
## ASV39 NA
## ASV40 NA
## ASV41 "Lachnospiraceae UCG-001"
## ASV42 "Acinetobacter"
## ASV43 "Roseburia"
## ASV44 "Lachnoclostridium"
## ASV45 "Bacillus"
## ASV46 NA
## ASV47 "A2"
## ASV48 NA
## ASV49 NA
## ASV50 "Incertae Sedis"
## ASV51 "Helicobacter"
## ASV52 "Lachnospiraceae UCG-001"
## ASV53 "[Eubacterium] nodatum group"
## ASV54 "Lachnospiraceae NK4A136 group"
## ASV55 NA
## ASV56 "Incertae Sedis"
## ASV57 "Lachnospiraceae NK4A136 group"
## ASV58 "Lachnoclostridium"
## ASV59 "Anaeroplasma"
## ASV60 "Actinomyces"
## ASV61 NA
## ASV62 NA
## ASV63 "Clostridium sensu stricto 1"
## ASV64 "Neisseria"
## ASV65 "Intestinimonas"
## ASV66 "Lachnospiraceae NK4A136 group"
## ASV67 "Bifidobacterium"
## ASV68 NA
## ASV69 NA
## ASV70 "Bacteroides"
## ASV71 NA
## ASV72 "Roseburia"
## ASV73 "Lachnospiraceae UCG-004"
## ASV74 "Lachnospiraceae NK4A136 group"
## ASV75 "Clostridium sensu stricto 1"
## ASV76 "Roseburia"
## ASV77 "Lachnoclostridium"
## ASV78 "Lachnospiraceae FCS020 group"
## ASV79 NA
## ASV80 NA
## ASV81 NA
## ASV82 NA
## ASV83 "Streptococcus"
## ASV84 "Lachnospiraceae NK4A136 group"
## ASV85 "Escherichia-Shigella"
## ASV86 NA
## ASV87 "Roseburia"
## ASV88 "Lachnospiraceae NK4A136 group"
## ASV89 "Lachnospiraceae NK4A136 group"
## ASV90 "Lachnoclostridium"
## ASV91 "Enterococcus"
## ASV92 "Colidextribacter"
## ASV93 "Colidextribacter"
## ASV94 "Candidatus Saccharimonas"
## ASV95 NA
## ASV96 NA
## ASV97 "Lachnospiraceae UCG-006"
## ASV98 "Listeria"
## ASV99 NA
## ASV100 NA
## ASV101 NA
## ASV102 "Pseudomonas"
## ASV103 "Streptococcus"
## ASV104 "A2"
## ASV105 "A2"
## ASV106 NA
## ASV107 "Deinococcus"
## ASV108 NA
## ASV109 NA
## ASV110 "Anaerotruncus"
## ASV111 "Roseburia"
## ASV112 NA
## ASV113 "Porphyromonas"
## ASV114 "Colidextribacter"
## ASV115 NA
## ASV116 "[Eubacterium] xylanophilum group"
## ASV117 NA
## ASV118 "Lachnospiraceae FCS020 group"
## ASV119 "Lachnospiraceae NK4A136 group"
## ASV120 "A2"
## ASV121 "Roseburia"
## ASV122 "Roseburia"
## ASV123 "A2"
## ASV124 NA
## ASV125 "Lachnospiraceae UCG-006"
## ASV126 NA
## ASV127 "Lachnospiraceae UCG-001"
## ASV128 "Lachnospiraceae NK4A136 group"
## ASV129 "Roseburia"
## ASV130 NA
## ASV131 "Lachnospiraceae NK4A136 group"
## ASV132 "GCA-900066575"
## ASV133 "Colidextribacter"
## ASV134 NA
## ASV135 "Lachnospiraceae UCG-001"
## ASV136 NA
## ASV137 "ASF356"
## ASV138 NA
## ASV139 NA
## ASV140 NA
## ASV141 NA
## ASV142 "Pseudomonas"
## ASV143 NA
## ASV144 "Rhodobacter"
## ASV145 "Lachnoclostridium"
## ASV146 NA
## ASV147 NA
## ASV148 "Roseburia"
## ASV149 NA
## ASV150 "Family XIII UCG-001"
## ASV151 "Enterorhabdus"
## ASV152 NA
## ASV153 "Acetatifactor"
## ASV154 NA
## ASV155 NA
## ASV156 NA
## ASV157 NA
## ASV158 NA
## ASV159 "Lachnospiraceae NK4A136 group"
## ASV160 NA
## ASV161 "Oscillibacter"
## ASV162 NA
## ASV163 NA
## ASV164 "ASF356"
## ASV165 NA
## ASV166 "GCA-900066575"
## ASV167 "Tyzzerella"
## ASV168 NA
## ASV169 NA
## ASV170 NA
## ASV171 "Acetatifactor"
## ASV172 NA
## ASV173 "GCA-900066575"
## ASV174 NA
## ASV175 NA
## ASV176 "Lachnospiraceae NK4A136 group"
## ASV177 "Acetatifactor"
## ASV178 NA
## ASV179 "Roseburia"
## ASV180 NA
## ASV181 NA
## ASV182 "Lachnoclostridium"
## ASV183 "Akkermansia"
## ASV184 "Enterorhabdus"
## ASV185 NA
## ASV186 NA
## ASV187 "Butyricicoccus"
## ASV188 "Streptococcus"
## ASV189 NA
## ASV190 "Candidatus Saccharimonas"
## ASV191 "GCA-900066575"
## ASV192 NA
## ASV193 "Roseburia"
## ASV194 NA
## ASV195 NA
## ASV196 "Lachnospiraceae NK4B4 group"
## ASV197 NA
## ASV198 NA
## ASV199 "Streptococcus"
## ASV200 "Candidatus Arthromitus"
## ASV201 NA
## ASV202 NA
## ASV203 NA
## ASV204 NA
## ASV205 NA
## ASV206 "Candidatus Stoquefichus"
## ASV207 "Roseburia"
## ASV208 "Lachnoclostridium"
## ASV209 NA
## ASV210 "Lachnospiraceae FCS020 group"
## ASV211 "Streptococcus"
## ASV212 "Anaerotruncus"
## ASV213 "Intestinimonas"
## ASV214 "Intestinimonas"
## ASV215 "Streptococcus"
## ASV216 "[Eubacterium] xylanophilum group"
## ASV217 NA
## ASV218 NA
## ASV219 NA
## ASV220 "GCA-900066575"
## ASV221 NA
## ASV222 NA
## ASV223 NA
## ASV224 "Coriobacteriaceae UCG-002"
## ASV225 NABasics of phyloseq
The below functions will enable accessing the object within the phyloseq.
sample_names(phyloseq)## [1] "F3D0" "F3D1" "F3D141" "F3D142" "F3D143" "F3D144" "F3D145" "F3D146"
## [9] "F3D147" "F3D148" "F3D149" "F3D150" "F3D2" "F3D3" "F3D5" "F3D6"
## [17] "F3D7" "F3D8" "F3D9"taxa_names(phyloseq)## [1] "ASV1" "ASV2" "ASV3" "ASV4" "ASV5" "ASV6" "ASV7" "ASV8"
## [9] "ASV9" "ASV10" "ASV11" "ASV12" "ASV13" "ASV14" "ASV15" "ASV16"
## [17] "ASV17" "ASV18" "ASV19" "ASV20" "ASV21" "ASV22" "ASV23" "ASV24"
## [25] "ASV25" "ASV26" "ASV27" "ASV28" "ASV29" "ASV30" "ASV31" "ASV32"
## [33] "ASV33" "ASV34" "ASV35" "ASV36" "ASV37" "ASV38" "ASV39" "ASV40"
## [41] "ASV41" "ASV42" "ASV43" "ASV44" "ASV45" "ASV46" "ASV47" "ASV48"
## [49] "ASV49" "ASV50" "ASV51" "ASV52" "ASV53" "ASV54" "ASV55" "ASV56"
## [57] "ASV57" "ASV58" "ASV59" "ASV60" "ASV61" "ASV62" "ASV63" "ASV64"
## [65] "ASV65" "ASV66" "ASV67" "ASV68" "ASV69" "ASV70" "ASV71" "ASV72"
## [73] "ASV73" "ASV74" "ASV75" "ASV76" "ASV77" "ASV78" "ASV79" "ASV80"
## [81] "ASV81" "ASV82" "ASV83" "ASV84" "ASV85" "ASV86" "ASV87" "ASV88"
## [89] "ASV89" "ASV90" "ASV91" "ASV92" "ASV93" "ASV94" "ASV95" "ASV96"
## [97] "ASV97" "ASV98" "ASV99" "ASV100" "ASV101" "ASV102" "ASV103" "ASV104"
## [105] "ASV105" "ASV106" "ASV107" "ASV108" "ASV109" "ASV110" "ASV111" "ASV112"
## [113] "ASV113" "ASV114" "ASV115" "ASV116" "ASV117" "ASV118" "ASV119" "ASV120"
## [121] "ASV121" "ASV122" "ASV123" "ASV124" "ASV125" "ASV126" "ASV127" "ASV128"
## [129] "ASV129" "ASV130" "ASV131" "ASV132" "ASV133" "ASV134" "ASV135" "ASV136"
## [137] "ASV137" "ASV138" "ASV139" "ASV140" "ASV141" "ASV142" "ASV143" "ASV144"
## [145] "ASV145" "ASV146" "ASV147" "ASV148" "ASV149" "ASV150" "ASV151" "ASV152"
## [153] "ASV153" "ASV154" "ASV155" "ASV156" "ASV157" "ASV158" "ASV159" "ASV160"
## [161] "ASV161" "ASV162" "ASV163" "ASV164" "ASV165" "ASV166" "ASV167" "ASV168"
## [169] "ASV169" "ASV170" "ASV171" "ASV172" "ASV173" "ASV174" "ASV175" "ASV176"
## [177] "ASV177" "ASV178" "ASV179" "ASV180" "ASV181" "ASV182" "ASV183" "ASV184"
## [185] "ASV185" "ASV186" "ASV187" "ASV188" "ASV189" "ASV190" "ASV191" "ASV192"
## [193] "ASV193" "ASV194" "ASV195" "ASV196" "ASV197" "ASV198" "ASV199" "ASV200"
## [201] "ASV201" "ASV202" "ASV203" "ASV204" "ASV205" "ASV206" "ASV207" "ASV208"
## [209] "ASV209" "ASV210" "ASV211" "ASV212" "ASV213" "ASV214" "ASV215" "ASV216"
## [217] "ASV217" "ASV218" "ASV219" "ASV220" "ASV221" "ASV222" "ASV223" "ASV224"
## [225] "ASV225"rank_names(phyloseq)## [1] "Kingdom" "Phylum" "Class" "Order" "Family" "Genus"rank_names(phyloseq)## [1] "Kingdom" "Phylum" "Class" "Order" "Family" "Genus"Summary of phyloseq object
Create table, number of features for each phyla
table(tax_table(phyloseq)[, "Phylum"], exclude = NULL)##
## Actinobacteriota Bacteroidota Campylobacterota Cyanobacteria
## 6 19 1 3
## Deinococcota Firmicutes Patescibacteria Proteobacteria
## 1 185 2 7
## Verrucomicrobiota
## 1We can see that most of taxa were from Firmicutes phylum.
Making a table of prevalence will show you this.
# Compute prevalence of each feature, store as data.frame
prevdf = apply(X = otu_table(phyloseq),
MARGIN = ifelse(taxa_are_rows(phyloseq), yes = 1, no = 2),
FUN = function(x){sum(x > 0)})
# Add taxonomy and total read counts to this data.frame
prevdf = data.frame(Prevalence = prevdf,
TotalAbundance = taxa_sums(phyloseq),
tax_table(phyloseq))
plyr::ddply(prevdf, "Phylum", function(df1){cbind(mean(df1$Prevalence),sum(df1$Prevalence))}) %>%
rename(avg_reads = "1", prevalence = "2")## Phylum avg_reads prevalence
## 1 Actinobacteriota 4.666667 28
## 2 Bacteroidota 13.842105 263
## 3 Campylobacterota 0.000000 0
## 4 Cyanobacteria 1.666667 5
## 5 Deinococcota 1.000000 1
## 6 Firmicutes 6.648649 1230
## 7 Patescibacteria 7.500000 15
## 8 Proteobacteria 3.714286 26
## 9 Verrucomicrobiota 2.000000 2You ca do the same thing for other taxonomic ranks as well.
plyr::ddply(prevdf, "Family", function(df1){cbind(mean(df1$Prevalence),sum(df1$Prevalence))}) %>%
rename(avg_reads = "1", prevalence = "2")## Family avg_reads prevalence
## 1 [Eubacterium] coprostanoligenes group 3.0000000 3
## 2 Acholeplasmataceae 10.0000000 10
## 3 Actinomycetaceae 0.0000000 0
## 4 Akkermansiaceae 2.0000000 2
## 5 Anaerovoracaceae 13.5000000 27
## 6 Atopobiaceae 1.0000000 1
## 7 Bacillaceae 0.0000000 0
## 8 Bacteroidaceae 9.5000000 19
## 9 Bifidobacteriaceae 13.0000000 13
## 10 Butyricicoccaceae 2.0000000 2
## 11 Christensenellaceae 9.0000000 9
## 12 Clostridiaceae 4.3333333 13
## 13 Deinococcaceae 1.0000000 1
## 14 Eggerthellaceae 4.6666667 14
## 15 Enterobacteriaceae 6.0000000 6
## 16 Enterococcaceae 0.0000000 0
## 17 Erysipelatoclostridiaceae 3.0000000 3
## 18 Erysipelotrichaceae 15.0000000 15
## 19 Helicobacteraceae 0.0000000 0
## 20 Lachnospiraceae 6.8813559 812
## 21 Lactobacillaceae 18.6666667 56
## 22 Listeriaceae 0.0000000 0
## 23 Mitochondria 8.0000000 8
## 24 Moraxellaceae 1.0000000 1
## 25 Muribaculaceae 15.0000000 225
## 26 Neisseriaceae 2.0000000 2
## 27 Oscillospiraceae 7.4666667 112
## 28 Peptococcaceae 16.5000000 33
## 29 Porphyromonadaceae 0.0000000 0
## 30 Pseudomonadaceae 4.5000000 9
## 31 Rhodobacteraceae 0.0000000 0
## 32 Rikenellaceae 19.0000000 19
## 33 Ruminococcaceae 5.1111111 46
## 34 Saccharimonadaceae 7.5000000 15
## 35 Staphylococcaceae 0.0000000 0
## 36 Streptococcaceae 0.6666667 4
## 37 <NA> 4.5000000 90Pevalence filtering
In many literature, they filter taxa that is having low-prevalence (to remove sequencing errors). It is not neccessary, but to do that you can use the below code
First, we can visualize the prevalence of those taxa in each phylum as below.
# Subset to the remaining phyla
prevdf1 = subset(prevdf, Phylum %in% get_taxa_unique(phyloseq, "Phylum"))
ggplot(prevdf1, aes(TotalAbundance, Prevalence / nsamples(phyloseq) * 100,color=Phylum)) +
# Include a guess for parameter
geom_hline(yintercept = 0.05, alpha = 0.5, linetype = 2) +
geom_point(size = 2, alpha = 0.7) +
scale_x_log10() +
xlab("Total read counts") +
ylab("Prevalence (% samples)") +
facet_wrap(~Phylum) 
You can see some of taxa were low-prevalent.
prevalenceThreshold = 0.1 * nsamples(phyloseq)
prevalenceThreshold## [1] 1.9As we have less than 20 samples, 5% filtering cannot filter any taxa. So I temporarilly used 10% as prevalence cut.
taxa_to_keep = rownames(prevdf1)[(prevdf1$Prevalence >= prevalenceThreshold)]
phyloseq_filtered = prune_taxa(taxa_to_keep, phyloseq)We filtered 48 taxa, that they were having prevalecne lower than 1.9!
Now, let’s see how many genus do we have.
length(get_taxa_unique(phyloseq_filtered, taxonomic.rank = "Genus"))## [1] 40There are 40 genuses, and
tax_table(phyloseq_filtered) %>%
data.frame %>%
.$Genus %>%
table(useNA = "always")## .
## [Eubacterium] nodatum group [Eubacterium] xylanophilum group
## 1 1
## A2 Acetatifactor
## 5 3
## Akkermansia Alistipes
## 1 1
## Anaeroplasma Anaerotruncus
## 1 1
## ASF356 Bacteroides
## 2 1
## Bifidobacterium Butyricicoccus
## 1 1
## Candidatus Arthromitus Candidatus Saccharimonas
## 1 2
## Candidatus Stoquefichus Clostridium sensu stricto 1
## 1 2
## Colidextribacter Enterorhabdus
## 4 2
## Escherichia-Shigella Family XIII UCG-001
## 1 1
## GCA-900066575 HT002
## 4 1
## Incertae Sedis Intestinimonas
## 2 1
## Lachnoclostridium Lachnospiraceae FCS020 group
## 5 2
## Lachnospiraceae NK4A136 group Lachnospiraceae UCG-001
## 20 4
## Lachnospiraceae UCG-004 Lachnospiraceae UCG-006
## 1 2
## Lactobacillus Ligilactobacillus
## 1 1
## Neisseria Oscillibacter
## 1 3
## Pseudomonas Roseburia
## 1 11
## Streptococcus Turicibacter
## 1 1
## Tyzzerella <NA>
## 1 81We have multiple species within each Genera. And Quite many taxa were not annotated at Genus level.
Lets remove taxa without Genus assignment
phyloseq_genus = tax_glom(phyloseq_filtered, "Genus", NArm = TRUE)Relative abundacne
Now, we can look at their abundance barplot.
plot_bar(phyloseq_genus, fill = "Genus") +
ylab("Total read counts")
Alternatively,
# Create a df with all `Top 10 Genus` and flag the top 20
top <- phyloseq_genus %>% taxa_sums %>% sort(decreasing=TRUE) %>%
names %>% as.data.frame(labels=TRUE) %>% rename(`Top 10 Genus`=".") %>%
mutate(`Top 10 Genus`=as.factor(case_when( #create agg`Top 10 Genus` variable
row_number()<=10~`Top 10 Genus`,row_number()>10~'Other'
)
)
)
top## Top 10 Genus
## 1 ASV15
## 2 ASV5
## 3 ASV8
## 4 ASV11
## 5 ASV13
## 6 ASV26
## 7 ASV43
## 8 ASV16
## 9 ASV44
## 10 ASV21
## 11 Other
## 12 Other
## 13 Other
## 14 Other
## 15 Other
## 16 Other
## 17 Other
## 18 Other
## 19 Other
## 20 Other
## 21 Other
## 22 Other
## 23 Other
## 24 Other
## 25 Other
## 26 Other
## 27 Other
## 28 Other
## 29 Other
## 30 Other
## 31 Other
## 32 Other
## 33 Other
## 34 Other
## 35 Other
## 36 Other
## 37 Other
## 38 Other
## 39 Othertop_tax_table <- tax_table(phyloseq_genus) %>% data.frame() %>%
mutate(ASV = rownames(.),
`Top10Genus` = case_when(ASV %in% top$`Top 10 Genus` ~ Genus,
.default = "Others")
)
phyloseq_genus_top_10 <- merge_phyloseq(tax_table(as.matrix(top_tax_table)),
otu_table(phyloseq_genus),
sample_data(phyloseq_genus))
plot_bar(phyloseq_genus_top_10, fill = "Top10Genus") +
ylab("Total read counts")
As I thaught in the lecture, the sequencing dataset’s total read counts
does not mean something. It need to be noralized to
relative abundance unless its sequencing procedure is
contianing internal standards (i.e., spiek-ins) or other data such as
ddPCR/PCR abundance estimates.
phyloseq_rel <- transform_sample_counts(phyloseq_genus_top_10, function(x){x/sum(x)})plot_bar(phyloseq_rel, fill = "Top10Genus") +
ylab("Total read counts")
We had one variable! Can we facet the plot by its sample data.
plot_bar(phyloseq_rel, fill = "Top10Genus") +
ylab("Total read counts") +
facet_wrap(~When, scales = "free")
With more functions, we can make the plot prettier
plot_bar(phyloseq_rel, fill = "Top10Genus") +
ylab("Total read counts") +
theme_classic() +
theme(axis.text.x = element_text(angle = 90)) +
scale_fill_brewer(type = "qual", palette = 3) +
facet_wrap(~When, scales = "free") +
ggtitle("Microbiome composition by sampling event time")
Can you see the difference?
Of course ifyou not. We need to calculate some simple matrices so that a number can represent the data at once.
microbiome::diversity() function with a phyloseqobject
as a input, will generate multiple alpha-diveristy indices at once!
microbiome::alpha(phyloseq_rel)## observed chao1 diversity_inverse_simpson diversity_gini_simpson
## F3D0 27 27 6.055101 0.8348500
## F3D1 27 27 5.473731 0.8173092
## F3D141 20 20 7.311927 0.8632371
## F3D142 14 14 6.118230 0.8365540
## F3D143 20 20 8.458811 0.8817801
## F3D144 18 18 6.641652 0.8494351
## F3D145 24 24 6.477691 0.8456240
## F3D146 22 22 8.536879 0.8828612
## F3D147 27 27 9.572472 0.8955338
## F3D148 27 27 7.532499 0.8672419
## F3D149 27 27 9.309459 0.8925824
## F3D150 21 21 8.317748 0.8797752
## F3D2 33 33 6.532057 0.8469089
## F3D3 21 21 6.827747 0.8535388
## F3D5 24 24 5.415914 0.8153590
## F3D6 27 27 7.339601 0.8637528
## F3D7 19 19 4.996238 0.7998494
## F3D8 27 27 6.762416 0.8521238
## F3D9 26 26 6.356050 0.8426696
## diversity_shannon diversity_coverage evenness_camargo evenness_pielou
## F3D0 2.443989 3 0.3421164 0.7415383
## F3D1 2.339922 3 0.3130526 0.7099630
## F3D141 2.292807 3 0.3554003 0.7653576
## F3D142 2.063371 3 0.4024161 0.7818592
## F3D143 2.453088 3 0.4195079 0.8188608
## F3D144 2.266895 3 0.3772324 0.7842918
## F3D145 2.255152 3 0.2924613 0.7096016
## F3D146 2.444567 3 0.3695040 0.7908553
## F3D147 2.605667 4 0.3682202 0.7905935
## F3D148 2.340649 3 0.2895153 0.7101834
## F3D149 2.552235 4 0.3494331 0.7743815
## F3D150 2.489153 3 0.4144107 0.8175841
## F3D2 2.388560 2 0.2603065 0.6831275
## F3D3 2.306098 3 0.3437111 0.7574579
## F3D5 2.239871 2 0.2964301 0.7047932
## F3D6 2.376133 3 0.2931972 0.7209500
## F3D7 2.051146 2 0.3015193 0.6966169
## F3D8 2.341600 3 0.2864801 0.7104720
## F3D9 2.298808 3 0.2858810 0.7055678
## evenness_simpson evenness_evar evenness_bulla dominance_dbp
## F3D0 0.2242630 0.3306606 0.5158717 0.3693158
## F3D1 0.2027308 0.2746231 0.4728233 0.3919032
## F3D141 0.3655963 0.3230793 0.4627127 0.2416918
## F3D142 0.4370164 0.3130210 0.5128205 0.2922824
## F3D143 0.4229406 0.4711282 0.5092036 0.2249561
## F3D144 0.3689807 0.3923232 0.5116564 0.3006135
## F3D145 0.2699038 0.2770593 0.3962795 0.2495854
## F3D146 0.3880400 0.3341278 0.4768462 0.2117040
## F3D147 0.3545360 0.3238547 0.4969390 0.1730104
## F3D148 0.2789814 0.2584735 0.3683532 0.1998404
## F3D149 0.3447948 0.3161600 0.4565414 0.1762267
## F3D150 0.3960832 0.4853761 0.5367347 0.2448980
## F3D2 0.1979411 0.2346582 0.3905340 0.2962048
## F3D3 0.3251308 0.3797586 0.4592154 0.2484433
## F3D5 0.2256631 0.3011122 0.4388391 0.3764783
## F3D6 0.2718371 0.2946045 0.4064334 0.2210829
## F3D7 0.2629599 0.2894241 0.4074074 0.3716108
## F3D8 0.2504598 0.2720016 0.4264568 0.2598684
## F3D9 0.2444634 0.3327522 0.4136307 0.2716636
## dominance_dmn dominance_absolute dominance_relative dominance_simpson
## F3D0 0.4470888 0.3693158 0.3693158 0.1651500
## F3D1 0.4699499 0.3919032 0.3919032 0.1826908
## F3D141 0.4199396 0.2416918 0.2416918 0.1367629
## F3D142 0.4548440 0.2922824 0.2922824 0.1634460
## F3D143 0.3673111 0.2249561 0.2249561 0.1182199
## F3D144 0.4392638 0.3006135 0.3006135 0.1505649
## F3D145 0.4917081 0.2495854 0.2495854 0.1543760
## F3D146 0.3648881 0.2117040 0.2117040 0.1171388
## F3D147 0.3302576 0.1730104 0.1730104 0.1044662
## F3D148 0.3741524 0.1998404 0.1998404 0.1327581
## F3D149 0.3244644 0.1762267 0.1762267 0.1074176
## F3D150 0.4081633 0.2448980 0.2448980 0.1202248
## F3D2 0.5078553 0.2962048 0.2962048 0.1530911
## F3D3 0.4819427 0.2484433 0.2484433 0.1464612
## F3D5 0.5111695 0.3764783 0.3764783 0.1846410
## F3D6 0.4150943 0.2210829 0.2210829 0.1362472
## F3D7 0.5398724 0.3716108 0.3716108 0.2001506
## F3D8 0.4797932 0.2598684 0.2598684 0.1478762
## F3D9 0.4881170 0.2716636 0.2716636 0.1573304
## dominance_core_abundance dominance_gini rarity_log_modulo_skewness
## F3D0 0.9689758 0.7502915 1.554475
## F3D1 0.9816361 0.7751809 1.872954
## F3D141 0.9894260 0.8102874 1.598483
## F3D142 0.9885057 0.8477117 1.506562
## F3D143 0.9912127 0.7712136 1.533253
## F3D144 0.9852761 0.8100676 1.366767
## F3D145 0.9834163 0.8122635 1.650961
## F3D146 0.9741824 0.7780573 1.485358
## F3D147 0.9780854 0.7353779 1.656629
## F3D148 0.9884324 0.7936751 1.862154
## F3D149 0.9737388 0.7517410 1.764083
## F3D150 0.9737609 0.7624530 1.439476
## F3D2 0.9733451 0.7779030 1.904880
## F3D3 0.9788294 0.8022480 1.624594
## F3D5 0.9737188 0.8079113 1.626114
## F3D6 0.9762100 0.7877201 1.891565
## F3D7 0.9928230 0.8449679 1.556327
## F3D8 0.9844925 0.7949200 1.861726
## F3D9 0.9729433 0.7977500 1.647142
## rarity_low_abundance rarity_rare_abundance
## F3D0 0.001274968 0.011049724
## F3D1 0.002086811 0.002921536
## F3D141 0.000000000 0.000000000
## F3D142 0.000000000 0.011494253
## F3D143 0.000000000 0.000000000
## F3D144 0.000000000 0.002453988
## F3D145 0.001658375 0.003316750
## F3D146 0.000000000 0.000000000
## F3D147 0.004998078 0.003460208
## F3D148 0.008376546 0.002792182
## F3D149 0.000000000 0.000000000
## F3D150 0.000000000 0.000000000
## F3D2 0.009885260 0.003353928
## F3D3 0.000000000 0.000000000
## F3D5 0.001314060 0.002628121
## F3D6 0.001640689 0.002871206
## F3D7 0.003189793 0.001594896
## F3D8 0.004229323 0.002819549
## F3D9 0.000000000 0.006946984Let’s add the diversity indices to original sample_data().
sample_data_with_alpha <-
phyloseq_rel %>%
sample_data() %>%
merge(., #Merge function will do the same thing as vloopup at excel
microbiome::alpha(phyloseq_rel),
by = 0) %>%
column_to_rownames("Row.names") %>%
sample_data
sample_data(phyloseq_rel) <- sample_data_with_alphaAlpha diversity boxplots
sample_data_with_alpha %>%
ggplot(aes(x = When, y = observed)) +
geom_boxplot() +
xlab("Species richness") +
theme_classic(base_size = 15)
As you can see, the alpha-diversity (species richenss) seemd to have different values.
sample_data_with_alpha %>%
ggplot(aes(x = When, y = diversity_inverse_simpson)) +
geom_boxplot() +
xlab("Inverse Simpson") +
theme_classic(base_size = 15)
sample_data_with_alpha %>%
ggplot(aes(x = When, y = diversity_shannon)) +
geom_boxplot() +
xlab("Inverse Simpson") +
theme_classic(base_size = 15)
sample_data_with_alpha %>%
ggplot(aes(x = When, y = dominance_dbp)) +
geom_boxplot() +
xlab("Berger Perker index") +
theme_classic(base_size = 15)
It seems like there are multiple different changes in alpha diversity!
How about Beta?
Distances between two samples, can be calculated in many ways.
Famous calculations, can be done with dist()
function
Beta diversity calculation
Bray-Curtis distnaces
phyloseq::distance(phyloseq_rel, method = "bray")## F3D0 F3D1 F3D141 F3D142 F3D143 F3D144 F3D145
## F3D1 0.1617363
## F3D141 0.5016585 0.5101768
## F3D142 0.6117886 0.6132388 0.4003778
## F3D143 0.5025906 0.4843155 0.2466802 0.2161918
## F3D144 0.5916932 0.6137586 0.3695281 0.4525049 0.3579027
## F3D145 0.5894426 0.6171674 0.3545452 0.3277006 0.2543390 0.2207622
## F3D146 0.3941444 0.3897431 0.2996539 0.5110689 0.3205143 0.3773640 0.3897923
## F3D147 0.4830239 0.4819109 0.3182267 0.3897137 0.2463592 0.2606685 0.2771466
## F3D148 0.5199403 0.5347185 0.1700583 0.3293065 0.2127113 0.3141956 0.2614451
## F3D149 0.4668561 0.4590682 0.1834836 0.3871171 0.1870551 0.3349880 0.3229820
## F3D150 0.3376365 0.3128712 0.2943821 0.3977749 0.2441448 0.4685769 0.4318809
## F3D2 0.2485925 0.1876468 0.4150413 0.5465322 0.4312941 0.6483347 0.6189519
## F3D3 0.5845165 0.5330330 0.2917073 0.3474962 0.2490386 0.4864710 0.3310007
## F3D5 0.2351819 0.1661146 0.4207296 0.5312526 0.4222672 0.5807099 0.5533829
## F3D6 0.3858591 0.3360574 0.4173695 0.3627506 0.3334254 0.5691067 0.4764460
## F3D7 0.5255556 0.4740683 0.4338552 0.3032778 0.2921884 0.5811117 0.4332722
## F3D8 0.3797454 0.3408312 0.3741496 0.3606538 0.2713762 0.5329299 0.3964817
## F3D9 0.3325041 0.3080068 0.3687184 0.3974766 0.2851277 0.5693409 0.4426190
## F3D146 F3D147 F3D148 F3D149 F3D150 F3D2 F3D3
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146
## F3D147 0.3151208
## F3D148 0.3314454 0.2183458
## F3D149 0.2910877 0.2485167 0.1617427
## F3D150 0.2557577 0.3357466 0.3289220 0.2506966
## F3D2 0.4153860 0.5068482 0.4497999 0.3993305 0.3114090
## F3D3 0.4607796 0.3852846 0.2930264 0.2850502 0.3663794 0.4269560
## F3D5 0.3899367 0.4731186 0.4397820 0.3949387 0.2940794 0.2228297 0.4843115
## F3D6 0.3556843 0.3768053 0.4151169 0.4033297 0.2518820 0.3046959 0.4094132
## F3D7 0.5032612 0.4392937 0.3938427 0.3883225 0.3917516 0.4018519 0.2847218
## F3D8 0.3692703 0.3576776 0.3646637 0.3481337 0.2380601 0.2851322 0.2818033
## F3D9 0.3639325 0.3874616 0.3768846 0.3739463 0.2316304 0.2128126 0.3429557
## F3D5 F3D6 F3D7 F3D8
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146
## F3D147
## F3D148
## F3D149
## F3D150
## F3D2
## F3D3
## F3D5
## F3D6 0.3113412
## F3D7 0.4349393 0.2977883
## F3D8 0.3159445 0.1844183 0.2157382
## F3D9 0.2594025 0.1775646 0.2520974 0.1174927Jaccard distnaces
phyloseq::distance(phyloseq_rel, method = "jaccard")## F3D0 F3D1 F3D141 F3D142 F3D143 F3D144 F3D145
## F3D1 0.2784389
## F3D141 0.6681393 0.6756518
## F3D142 0.7591425 0.7602579 0.5718139
## F3D143 0.6689655 0.6525776 0.3957393 0.3555225
## F3D144 0.7434764 0.7606573 0.5396430 0.6230683 0.5271404
## F3D145 0.7416973 0.7632696 0.5234897 0.4936363 0.4055347 0.3616793
## F3D146 0.5654283 0.5608851 0.4611288 0.6764336 0.4854386 0.5479510 0.5609360
## F3D147 0.6514040 0.6503912 0.4828103 0.5608547 0.3953262 0.4135401 0.4340090
## F3D148 0.6841589 0.6968294 0.2906834 0.4954561 0.3508028 0.4781565 0.4145168
## F3D149 0.6365398 0.6292622 0.3100737 0.5581607 0.3151582 0.5018592 0.4882636
## F3D150 0.5048255 0.4766213 0.4548612 0.5691544 0.3924700 0.6381374 0.6032358
## F3D2 0.3981963 0.3159977 0.5866137 0.7067841 0.6026632 0.7866542 0.7646328
## F3D3 0.7377853 0.6953966 0.4516616 0.5157657 0.3987685 0.6545314 0.4973711
## F3D5 0.3808053 0.2849027 0.5922726 0.6938798 0.5937945 0.7347457 0.7124874
## F3D6 0.5568519 0.5030584 0.5889353 0.5323800 0.5001035 0.7253894 0.6453958
## F3D7 0.6890022 0.6432108 0.6051590 0.4654077 0.4522380 0.7350673 0.6045917
## F3D8 0.5504572 0.5083879 0.5445544 0.5301184 0.4269015 0.6953089 0.5678294
## F3D9 0.4990665 0.4709560 0.5387791 0.5688490 0.4437344 0.7255796 0.6136326
## F3D146 F3D147 F3D148 F3D149 F3D150 F3D2 F3D3
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146
## F3D147 0.4792271
## F3D148 0.4978731 0.3584299
## F3D149 0.4509186 0.3980991 0.2784484
## F3D150 0.4073361 0.5027100 0.4950207 0.4008912
## F3D2 0.5869579 0.6727263 0.6204993 0.5707451 0.4749228
## F3D3 0.6308681 0.5562533 0.4532411 0.4436406 0.5362777 0.5984150
## F3D5 0.5610855 0.6423361 0.6109008 0.5662453 0.4544998 0.3644493 0.6525739
## F3D6 0.5247303 0.5473618 0.5866892 0.5748182 0.4024054 0.4670757 0.5809697
## F3D7 0.6695592 0.6104295 0.5651179 0.5594126 0.5629620 0.5733158 0.4432427
## F3D8 0.5393680 0.5268963 0.5344375 0.5164677 0.3845695 0.4437399 0.4396982
## F3D9 0.5336518 0.5585186 0.5474455 0.5443391 0.3761363 0.3509406 0.5107476
## F3D5 F3D6 F3D7 F3D8
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146
## F3D147
## F3D148
## F3D149
## F3D150
## F3D2
## F3D3
## F3D5
## F3D6 0.4748440
## F3D7 0.6062129 0.4589167
## F3D8 0.4801790 0.3114074 0.3549090
## F3D9 0.4119453 0.3015793 0.4026802 0.2102792Bray-Curtis distnaces
phyloseq::distance(phyloseq_rel, method = "horn")## F3D0 F3D1 F3D141 F3D142 F3D143 F3D144
## F3D1 0.02293791
## F3D141 0.31440360 0.32879875
## F3D142 0.48435499 0.49063321 0.22965562
## F3D143 0.39431481 0.39675127 0.10886823 0.06834966
## F3D144 0.57294881 0.55785661 0.29741570 0.38456741 0.23887811
## F3D145 0.58013274 0.58069159 0.20912368 0.19266782 0.09784677 0.08300786
## F3D146 0.23906577 0.23853859 0.18773184 0.32672592 0.17323649 0.23148743
## F3D147 0.36985596 0.37663599 0.23652116 0.21405417 0.10501787 0.11887282
## F3D148 0.35924358 0.37731801 0.03466328 0.17842858 0.06106949 0.19431600
## F3D149 0.36038892 0.35842308 0.05220906 0.21809442 0.06146666 0.21125792
## F3D150 0.13571572 0.13691079 0.13414015 0.20773123 0.11417299 0.39649607
## F3D2 0.09459553 0.08556185 0.17873477 0.39289127 0.30500147 0.59927745
## F3D3 0.50596202 0.50248736 0.11856858 0.12317124 0.07612092 0.38793833
## F3D5 0.04150792 0.02677851 0.23119795 0.39710106 0.31155289 0.51947519
## F3D6 0.23380305 0.21172668 0.26161901 0.13709554 0.15405099 0.52430577
## F3D7 0.46502508 0.46760567 0.26550304 0.08257750 0.13189334 0.53899005
## F3D8 0.23643511 0.23980404 0.18028080 0.13046821 0.11186190 0.49510460
## F3D9 0.15209129 0.15297836 0.15318324 0.17465415 0.14584728 0.51012265
## F3D145 F3D146 F3D147 F3D148 F3D149 F3D150
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146 0.20729215
## F3D147 0.10876672 0.13338698
## F3D148 0.11080695 0.19269561 0.14580677
## F3D149 0.14150629 0.16652800 0.14480426 0.03236356
## F3D150 0.30522564 0.11610818 0.17803641 0.15218762 0.12308623
## F3D2 0.54568199 0.27314423 0.42597371 0.26335625 0.24730294 0.11903613
## F3D3 0.17921961 0.30781849 0.28385278 0.10244433 0.10312381 0.20931376
## F3D5 0.49294253 0.22448788 0.34181816 0.27646047 0.28861883 0.10604831
## F3D6 0.38607726 0.23770124 0.25914410 0.27947942 0.25398092 0.08419785
## F3D7 0.26775087 0.34050361 0.32513626 0.24286750 0.27320874 0.21409587
## F3D8 0.29833330 0.19743583 0.24126987 0.18893736 0.19448643 0.07131076
## F3D9 0.34872402 0.18145326 0.27541947 0.19011435 0.20242412 0.05202218
## F3D2 F3D3 F3D5 F3D6 F3D7 F3D8
## F3D1
## F3D141
## F3D142
## F3D143
## F3D144
## F3D145
## F3D146
## F3D147
## F3D148
## F3D149
## F3D150
## F3D2
## F3D3 0.32557820
## F3D5 0.05466903 0.39499616
## F3D6 0.17712478 0.22782074 0.17829804
## F3D7 0.37047276 0.09981207 0.36452275 0.15149821
## F3D8 0.18875677 0.12889512 0.17431440 0.06735324 0.06707938
## F3D9 0.10059747 0.18152390 0.09097087 0.06272670 0.12550318 0.02461637These distances, cannot be displayed in single pannel as they are having multiple dimensions. Then need to be ordinated (scaled-down to 2 dimension).
###{-}
Ordination
Principal Coordinates Analysis with Bray-Curtis dist
plot_ordination(physeq = phyloseq_rel,
ordination = ordinate(phyloseq_rel, "PCoA", "bray"),
col = "When"
)
Principal Coordinates Analysis with Bray-Curtis dist
plot_ordination(physeq = phyloseq_rel,
ordination = ordinate(phyloseq_rel, "MDS", "jaccard"),
col = "When"
)
Redundancy analysis (RDA) with Morisita-Horn index
plot_ordination(physeq = phyloseq_rel,
ordination = ordinate(phyloseq_rel, "RDA", "horn"),
col = "When"
)
PCA with Morisita-Horn index
plot_ordination(physeq = phyloseq_rel,
ordination = ordinate(phyloseq_rel, "RDA", "horn"),
col = "When"
) +
stat_ellipse(type = "norm", linetype = 2) +
stat_ellipse(type = "t") +
theme_classic() +
scale_color_brewer(type = "qual")
Species richness was different across samples. Was there a effect of sequencing depth?
Calculating total reads
sample_data(phyloseq_rel)$total_reads <- sample_sums(phyloseq_filtered)
sample_data(phyloseq_rel)## Subject Gender Day When observed chao1 diversity_inverse_simpson
## F3D0 3 F 0 Early 27 27 6.055101
## F3D1 3 F 1 Early 27 27 5.473731
## F3D141 3 F 141 Late 20 20 7.311927
## F3D142 3 F 142 Late 14 14 6.118230
## F3D143 3 F 143 Late 20 20 8.458811
## F3D144 3 F 144 Late 18 18 6.641652
## F3D145 3 F 145 Late 24 24 6.477691
## F3D146 3 F 146 Late 22 22 8.536879
## F3D147 3 F 147 Late 27 27 9.572472
## F3D148 3 F 148 Late 27 27 7.532499
## F3D149 3 F 149 Late 27 27 9.309459
## F3D150 3 F 150 Late 21 21 8.317748
## F3D2 3 F 2 Early 33 33 6.532057
## F3D3 3 F 3 Early 21 21 6.827747
## F3D5 3 F 5 Early 24 24 5.415914
## F3D6 3 F 6 Early 27 27 7.339601
## F3D7 3 F 7 Early 19 19 4.996238
## F3D8 3 F 8 Early 27 27 6.762416
## F3D9 3 F 9 Early 26 26 6.356050
## diversity_gini_simpson diversity_shannon diversity_coverage
## F3D0 0.8348500 2.443989 3
## F3D1 0.8173092 2.339922 3
## F3D141 0.8632371 2.292807 3
## F3D142 0.8365540 2.063371 3
## F3D143 0.8817801 2.453088 3
## F3D144 0.8494351 2.266895 3
## F3D145 0.8456240 2.255152 3
## F3D146 0.8828612 2.444567 3
## F3D147 0.8955338 2.605667 4
## F3D148 0.8672419 2.340649 3
## F3D149 0.8925824 2.552235 4
## F3D150 0.8797752 2.489153 3
## F3D2 0.8469089 2.388560 2
## F3D3 0.8535388 2.306098 3
## F3D5 0.8153590 2.239871 2
## F3D6 0.8637528 2.376133 3
## F3D7 0.7998494 2.051146 2
## F3D8 0.8521238 2.341600 3
## F3D9 0.8426696 2.298808 3
## evenness_camargo evenness_pielou evenness_simpson evenness_evar
## F3D0 0.3421164 0.7415383 0.2242630 0.3306606
## F3D1 0.3130526 0.7099630 0.2027308 0.2746231
## F3D141 0.3554003 0.7653576 0.3655963 0.3230793
## F3D142 0.4024161 0.7818592 0.4370164 0.3130210
## F3D143 0.4195079 0.8188608 0.4229406 0.4711282
## F3D144 0.3772324 0.7842918 0.3689807 0.3923232
## F3D145 0.2924613 0.7096016 0.2699038 0.2770593
## F3D146 0.3695040 0.7908553 0.3880400 0.3341278
## F3D147 0.3682202 0.7905935 0.3545360 0.3238547
## F3D148 0.2895153 0.7101834 0.2789814 0.2584735
## F3D149 0.3494331 0.7743815 0.3447948 0.3161600
## F3D150 0.4144107 0.8175841 0.3960832 0.4853761
## F3D2 0.2603065 0.6831275 0.1979411 0.2346582
## F3D3 0.3437111 0.7574579 0.3251308 0.3797586
## F3D5 0.2964301 0.7047932 0.2256631 0.3011122
## F3D6 0.2931972 0.7209500 0.2718371 0.2946045
## F3D7 0.3015193 0.6966169 0.2629599 0.2894241
## F3D8 0.2864801 0.7104720 0.2504598 0.2720016
## F3D9 0.2858810 0.7055678 0.2444634 0.3327522
## evenness_bulla dominance_dbp dominance_dmn dominance_absolute
## F3D0 0.5158717 0.3693158 0.4470888 0.3693158
## F3D1 0.4728233 0.3919032 0.4699499 0.3919032
## F3D141 0.4627127 0.2416918 0.4199396 0.2416918
## F3D142 0.5128205 0.2922824 0.4548440 0.2922824
## F3D143 0.5092036 0.2249561 0.3673111 0.2249561
## F3D144 0.5116564 0.3006135 0.4392638 0.3006135
## F3D145 0.3962795 0.2495854 0.4917081 0.2495854
## F3D146 0.4768462 0.2117040 0.3648881 0.2117040
## F3D147 0.4969390 0.1730104 0.3302576 0.1730104
## F3D148 0.3683532 0.1998404 0.3741524 0.1998404
## F3D149 0.4565414 0.1762267 0.3244644 0.1762267
## F3D150 0.5367347 0.2448980 0.4081633 0.2448980
## F3D2 0.3905340 0.2962048 0.5078553 0.2962048
## F3D3 0.4592154 0.2484433 0.4819427 0.2484433
## F3D5 0.4388391 0.3764783 0.5111695 0.3764783
## F3D6 0.4064334 0.2210829 0.4150943 0.2210829
## F3D7 0.4074074 0.3716108 0.5398724 0.3716108
## F3D8 0.4264568 0.2598684 0.4797932 0.2598684
## F3D9 0.4136307 0.2716636 0.4881170 0.2716636
## dominance_relative dominance_simpson dominance_core_abundance
## F3D0 0.3693158 0.1651500 0.9689758
## F3D1 0.3919032 0.1826908 0.9816361
## F3D141 0.2416918 0.1367629 0.9894260
## F3D142 0.2922824 0.1634460 0.9885057
## F3D143 0.2249561 0.1182199 0.9912127
## F3D144 0.3006135 0.1505649 0.9852761
## F3D145 0.2495854 0.1543760 0.9834163
## F3D146 0.2117040 0.1171388 0.9741824
## F3D147 0.1730104 0.1044662 0.9780854
## F3D148 0.1998404 0.1327581 0.9884324
## F3D149 0.1762267 0.1074176 0.9737388
## F3D150 0.2448980 0.1202248 0.9737609
## F3D2 0.2962048 0.1530911 0.9733451
## F3D3 0.2484433 0.1464612 0.9788294
## F3D5 0.3764783 0.1846410 0.9737188
## F3D6 0.2210829 0.1362472 0.9762100
## F3D7 0.3716108 0.2001506 0.9928230
## F3D8 0.2598684 0.1478762 0.9844925
## F3D9 0.2716636 0.1573304 0.9729433
## dominance_gini rarity_log_modulo_skewness rarity_low_abundance
## F3D0 0.7502915 1.554475 0.001274968
## F3D1 0.7751809 1.872954 0.002086811
## F3D141 0.8102874 1.598483 0.000000000
## F3D142 0.8477117 1.506562 0.000000000
## F3D143 0.7712136 1.533253 0.000000000
## F3D144 0.8100676 1.366767 0.000000000
## F3D145 0.8122635 1.650961 0.001658375
## F3D146 0.7780573 1.485358 0.000000000
## F3D147 0.7353779 1.656629 0.004998078
## F3D148 0.7936751 1.862154 0.008376546
## F3D149 0.7517410 1.764083 0.000000000
## F3D150 0.7624530 1.439476 0.000000000
## F3D2 0.7779030 1.904880 0.009885260
## F3D3 0.8022480 1.624594 0.000000000
## F3D5 0.8079113 1.626114 0.001314060
## F3D6 0.7877201 1.891565 0.001640689
## F3D7 0.8449679 1.556327 0.003189793
## F3D8 0.7949200 1.861726 0.004229323
## F3D9 0.7977500 1.647142 0.000000000
## rarity_rare_abundance total_reads
## F3D0 0.011049724 6337
## F3D1 0.002921536 4843
## F3D141 0.000000000 4784
## F3D142 0.011494253 2495
## F3D143 0.000000000 2453
## F3D144 0.002453988 3440
## F3D145 0.003316750 5744
## F3D146 0.000000000 3827
## F3D147 0.003460208 12821
## F3D148 0.002792182 9780
## F3D149 0.000000000 10415
## F3D150 0.000000000 4285
## F3D2 0.003353928 16538
## F3D3 0.000000000 5368
## F3D5 0.002628121 3673
## F3D6 0.002871206 6595
## F3D7 0.001594896 4158
## F3D8 0.002819549 4435
## F3D9 0.006946984 5833Making plot of rarefaction curve
sample_data(phyloseq_rel) %>%
data.frame() %>%
ggplot(aes(x = total_reads, y = observed)) +
geom_point()
Color coding with sample data
sample_data(phyloseq_rel) %>%
data.frame() %>%
ggplot(aes(x = total_reads, y = observed, col = When)) +
geom_point() +
theme_classic()
It may needs further investigation.
Next lecture will cover how to analyze differences between those to groups statistically and how to run multivariate analysis!
Bibliography
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