View Full Table | Close Full ViewTable 1.

Ingredient composition as percentage of diet (DM basis)1

 
Item Late growing diet (Moderate Grain) Finishing diet (High Grain) Early growing diet (Silage/Forage)
Dry-rolled corn 66 82.75
Corn silage 26 12.75 70
Soybean meal 5.85
Alfalfa haylage 30
Supplement 12 2.15
Supplement 23 4.5
1All diets were formulated to exceed National Research Council recommendations for cattle (NRC, 1996).
2Custom supplement included (% DM) 62.55% limestone, 2.38% NaCl, 32.63% urea, 0.93% trace mineral mix (13% Ca, 12% Zn, 8% Mn, 10% Zn, 1.5% Cu, 0.2% I, and 0.1% Co), 0.56% vitamin mix (A 8,818,490 IU/kg, D 881,849 IU/kg, and E 882 IU/kg), and 0.95% Rumensin-80 (Elanco Animal Health, Indianapolis, IN).
3Commercial supplement (Biegert Feeds, Bradshaw, NE) included (% DM) 32% CP (28% NPN), 7.5% Ca, 0.8% P, 4.8% NaCl, 1.8% K, 55,116 IU/kg vitamin A, 105 IU/kg vitamin E, and 0.065% sodium monensin (Elanco Animal Health, Indianapolis, IN).



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Diversity statistics

 
Maximum no. of OTU
Diet type Sample type No. of cleaned sequences No. of observed OTU1 Chao1 ACE Shannon diversity index
Moderate Grain (n = 142) Pooled sample 1,035,186 109,984 214,992 303,111 8.64
Range of individual samples 3,132–11,702 1,432–5,048 4,048–20,171 7,165–46,185 6.33–7.67
Range of individual subsamples2 2,000 1,184 ± 11a 5,734 ± 90a 13,929 ± 254a 6.53 ± 0.03a
High Grain (n = 130) Pooled sample 877,232 67,469 167,616 278,239 7.01
Range of individual samples 2,055–14,770 584–3,643 1,101–11,977 1,330–23,750 4.34–7.00
Range of individual subsamples2 2,000 690 ± 12c 2,253 ± 94c 4,382 ± 265c 5.40 ± 0.03c
Silage/Forage (n = 61) Pooled sample 236,590 35,341 101,211 183,344 7.49
Range of individual samples 2,004–13,598 632–4,238 1,575–15,101 2,543–35,795 4.15–7.39
Range of individual subsamples2 2,000 943 ± 17b 3,570 ± 138b 7,566 ± 387b 5.88 ± 0.05b
a,b,cWithin a column, means for the range of individual subsamples having differing superscripts differ (P < 0.05).
1OTU = operational taxonomic units.
2Means among 3 diet groups were compared using ANOVA followed by the Tukey’s test.



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Relative abundance of dominant taxa in 3 diet groups

 
Percentage of total sequences1
Classification Collective data2 Moderate Grain High Grain Silage/Forage SEM P-value3 No. of cattle with detectable taxon4
Firmicutes 64.33 50.31c 76.91a 70.15b 0.82 0.001 333
    Oscillibacter 5.20 4.57b 8.10a 0.65c 0.21 0.001 332
    Turicibacter 4.62 1.26c 8.40a 4.37b 0.29 0.001 333
    Roseburia 3.39 3.94a 4.21a 0.38b 0.11 0.001 327
    Fecalibacterium 2.43 4.06a 1.78b 0.05c 0.14 0.001 274
    Coprococcus 2.33 2.37b 2.94a 0.95c 0.07 0.001 330
    Clostridium 1.86 1.13b 2.92a 1.29b 0.07 0.001 333
    Sporacetigenium 0.40 0.19c 0.36b 1.01a 0.02 0.001 332
    Blautia 0.78 0.22b 1.73a 0.06b 0.06 0.001 294
    Lactobacillus 0.72 0.27b 1.50a 0.13b 0.09 0.001 315
    Subdoligranulum 0.35 0.29b 0.56a 0.05c 0.02 0.001 273
    Microbacterium 0.35 0.05b 0.54a 0.63a 0.04 0.001 188
    Anaerovibrio 0.52 0.96a 0.25b 0.05c 0.03 0.001 275
    Anaerovorax 0.31 0.12c 0.31b 0.75a 0.02 0.001 318
    Ruminococcus 0.24 0.11b 0.32a 0.39a 0.02 0.001 325
    Unclassified Ruminococcaceae 15.19 8.12c 14.63b 32.86a 0.59 0.001 333
    Unclassified Lachnospiraceae 12.15 12.98a 12.71a 9.06b 0.19 0.001 333
    Unclassified Clostridiales 6.78 5.78c 6.75b 9.20a 0.13 0.001 333
    Unclassified Peptostreptococcaceae 2.57 0.68c 4.40a 3.07b 0.14 0.001 333
    Unclassified Erysipelotrichaceae 0.45 0.23c 0.41b 1.03a 0.02 0.001 333
    Unclassified Veillonellaceae 0.31 0.60a 0.12b 0.05b 0.02 0.001 258
    Unclassified Clostridia 0.39 0.20b 0.57a 0.45a 0.02 0.001 332
    Unclassified Clostridiaceae 0.40 0.48a 0.31b 0.39b 0.01 0.001 330
    Unclassified Firmicutes 1.16 0.90c 1.06b 1.96a 0.03 0.001 333
Bacteroidetes 21.28 37.39a 12.82b 1.83c 0.89 0.001 333
    Prevotella 6.99 14.39a 2.15b 0.09c 0.42 0.001 318
    Bacteroides 0.72 0.97a 0.77a 0.06b 0.05 0.001 277
    Parabacteroides 0.61 0.88a 0.59b 0.05c 0.03 0.001 274
    Unclassified Prevotellaceae 5.89 10.69a 3.37b 0.07c 0.29 0.001 301
    Unclassified Porphyromonadaceae 2.23 2.84a 2.55a 0.12b 0.11 0.001 301
    Unclassified Bacteroidales 1.95 3.44a 1.09b 0.32c 0.09 0.001 323
    Unclassified Bacteroidetes 2.67 3.81a 2.15b 1.16c 0.13 0.001 331
Proteobacteria 3.53 6.04a 1.30b 2.43b 0.21 0.001 333
    Succinivibrio 2.08 4.46a 0.43b 0.05b 0.14 0.001 267
    Pantoea 0.28 0.58a 0.05b 0.05b 0.03 0.001 111
TM7 2.32 0.24b 0.56b 10.92a 0.24 0.001 329
    TM7 genera incertae sedis 2.32 0.24b 0.56b 10.92a 0.24 0.001 329
Actinobacteria 1.28 0.14c 1.77b 2.93a 0.11 0.001 330
    Propionibacterium 0.18 0.05b 0.08b 0.68a 0.04 0.001 123
    Unclassified Coriobacteriaceae 0.20 0.06c 0.22b 0.51a 0.01 0.001 269
Cyanobacteria 0.54 1.14a 0.09b 0.09b 0.06 0.001 189
    Streptophyta 0.54 1.14a 0.09b 0.09b 0.06 0.001 189
Verrucomicrobia 0.27 0.06b 0.10b 1.15a 0.04 0.001 123
    Akkermansia 0.27 0.06b 0.10b 1.14a 0.04 0.001 111
Unclassified Bacteria 6.22 4.51c 6.28b 10.07a 0.17 0.001 333
a,b,cWithin a row, means with a different subscript were different (P < 0.05).
1Values indicate means.
2Sequences obtained from all 333 fecal samples.
3A P-value of 0.001 is less than or equal to 0.001.
4Percentage of total sequences for cattle with nondetectable taxon was treated as 0.05%.



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Dominant operational taxonomic units (OTU) calculated from 333 subsamples in 3 diet groups

 
Percentage of total sequences1
No. OTU ID2 Classification Collective data3 Moderate Grain High Grain Silage/Forage SEM P-value4 No. of cattle with detectable taxon5
OTU-1153 Unclassified Bacteria 0.14 0.05b 0.05b 0.54a 0.02 0.001 96
OTU-1157 Unclassified Bacteria 0.36 0.08b 0.81a 0.05b 0.06 0.001 192
OTU-1158 Unclassified Bacteria 0.44 0.15b 0.93a 0.05b 0.04 0.001 263
OTU-1209 Propionibacterium 0.15 0.05b 0.07b 0.55a 0.04 0.001 98
OTU-1646 Unclassified Bacteroidetes 0.15 0.05b 0.05b 0.59a 0.06 0.001 29
OTU-1648 Unclassified Bacteroidetes 0.51 0.65a 0.59a 0.05b 0.03 0.001 268
OTU-1649 Unclassified Bacteroidetes 0.55 0.86a 0.44b 0.05c 0.05 0.001 256
OTU-1194 Microbacterium 0.34 0.05b 0.54a 0.62a 0.04 0.001 181
OTU-2601 Unclassified Porphyromonadaceae 0.29 0.20b 0.52a 0.05b 0.03 0.001 234
OTU-2602 Unclassified Porphyromonadaceae 0.39 0.54a 0.38b 0.05c 0.02 0.001 257
OTU-3869 Unclassified Prevotellaceae 0.37 0.72a 0.15b 0.05b 0.03 0.001 238
OTU-3870 Unclassified Prevotellaceae 0.39 0.05b 0.93a 0.05b 0.07 0.001 97
OTU-3872 Unclassified Prevotellaceae 0.65 1.39a 0.12b 0.05b 0.05 0.001 227
OTU-5060 Prevotella 0.35 0.70a 0.09b 0.05b 0.02 0.001 221
OTU-5061 Prevotella 0.39 0.77a 0.13b 0.05b 0.03 0.001 247
OTU-5062 Prevotella 0.68 1.33a 0.27b 0.05b 0.05 0.001 258
OTU-5135 Streptophyta 0.49 1.04a 0.08b 0.08b 0.06 0.001 171
OTU-5500 Lactobacillus 0.57 0.19b 1.22a 0.08b 0.08 0.001 296
OTU-7122 Unclassified Clostridiales 0.26 0.07c 0.16b 0.90a 0.02 0.001 320
OTU-7331 Clostridium 1.12 0.45b 2.19a 0.39b 0.06 0.001 331
OTU-9520 Unclassified Lachnospiraceae 0.15 0.05b 0.06b 0.57a 0.02 0.001 71
OTU-9522 Unclassified Lachnospiraceae 0.16 0.05b 0.05b 0.64a 0.02 0.001 117
OTU-9527 Unclassified Lachnospiraceae 0.30 0.19b 0.52a 0.11b 0.03 0.001 306
OTU-9528 Unclassified Lachnospiraceae 0.36 0.29b 0.57a 0.05c 0.03 0.001 259
OTU-9529 Unclassified Lachnospiraceae 0.40 0.05b 0.06b 1.94a 0.05 0.001 134
OTU-9530 Unclassified Lachnospiraceae 0.43 0.75a 0.26b 0.05c 0.02 0.001 263
OTU-9531 Unclassified Lachnospiraceae 1.65 0.86b 3.25a 0.05c 0.12 0.001 274
OTU-9760 Coprococcus 0.15 0.05b 0.06b 0.58a 0.02 0.001 106
OTU-9761 Coprococcus 0.36 0.58a 0.27b 0.05c 0.02 0.001 265
OTU-9762 Coprococcus 1.10 0.89b 1.82a 0.05c 0.06 0.001 272
OTU-10257 Roseburia 0.36 0.11b 0.77a 0.05b 0.04 0.001 263
OTU-10377 Unclassified Peptostreptococcaceae 0.28 0.09c 0.35b 0.55a 0.02 0.001 330
OTU-10378 Unclassified Peptostreptococcaceae 1.88 0.39c 3.79a 1.29b 0.13 0.001 333
OTU-12960 Unclassified Ruminococcaceae 0.19 0.05b 0.05b 0.82a 0.02 0.001 61
OTU-12962 Unclassified Ruminococcaceae 0.23 0.06b 0.10b 0.92a 0.03 0.001 201
OTU-12965 Unclassified Ruminococcaceae 0.25 0.17b 0.13b 0.67a 0.02 0.001 289
OTU-12966 Unclassified Ruminococcaceae 0.29 0.07b 0.63a 0.05b 0.02 0.001 248
OTU-12968 Unclassified Ruminococcaceae 0.35 0.09b 0.78a 0.05b 0.03 0.001 264
OTU-12969 Unclassified Ruminococcaceae 0.54 0.06b 0.07b 2.69a 0.07 0.001 158
OTU-12970 Unclassified Ruminococcaceae 0.53 0.09b 1.23a 0.05b 0.05 0.001 249
OTU-12971 Unclassified Ruminococcaceae 0.60 0.20b 1.25a 0.16b 0.04 0.001 327
OTU-12972 Unclassified Ruminococcaceae 0.61 0.67b 0.82a 0.05c 0.03 0.001 271
OTU-12973 Unclassified Ruminococcaceae 1.50 0.05b 0.12b 7.81a 0.21 0.001 159
OTU-13387 Fecalibacterium 1.02 1.38a 1.09b 0.05c 0.06 0.001 274
OTU-13994 Oscillibacter 0.27 0.15b 0.52a 0.05c 0.02 0.001 270
OTU-13995 Oscillibacter 0.33 0.14b 0.66a 0.05b 0.03 0.001 267
OTU-13996 Oscillibacter 0.36 0.33b 0.54a 0.05c 0.02 0.001 266
OTU-13997 Oscillibacter 0.44 0.16b 0.91a 0.05b 0.03 0.001 267
OTU-13998 Oscillibacter 1.00 0.29b 2.23a 0.05b 0.08 0.001 271
OTU-14605 Turicibacter 3.56 0.71c 6.72a 3.44b 0.24 0.001 333
OTU-14737 Helicobacter 0.26 0.05b 0.05b 1.18a 0.14 0.001 19
OTU-14977 Succinivibrio 1.26 2.60a 0.37b 0.05b 0.08 0.001 264
OTU-15034 Pantoea 0.24 0.50a 0.05b 0.05b 0.03 0.001 108
OTU-15452 TM7 genera incertae sedis 0.20 0.05b 0.08b 0.81a 0.02 0.001 171
OTU-15453 TM7 genera incertae sedis 0.22 0.05b 0.05b 0.94a 0.02 0.001 131
OTU-15486 Akkermansia 0.17 0.05b 0.10b 0.60a 0.03 0.001 84
a,b,cWithin a row, means with a different subscript were different (P < 0.05).
1Values represent means.
2A total of 176,692 OTU were numbered in serial order.
3Sequences obtained from all 333 fecal samples.
4A P-value of 0.001 is less than or equal to 0.001.
5Percentage of total sequences for cattle with nondetectable taxon was treated as 0.05%.