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. 2018 Jan 27;96(3):1017–1031. doi: 10.1093/jas/skx034

Table 3.

Abundance of core bacterial taxa in fecal samples of pigs fed control or SDPP diets

Taxonomy Day 0 Day 7 Day 14 Day 21 Day 28 SEM P-value
CTL1 SDPP2 CTL SDPP CTL SDPP CTL SDPP CTL SDPP trt3 Day trt×day
Phylum
 Firmicutes 59.49 65.73 79.57 72.84 82.30 80.81 90.32 92.05 93.02 90.98 4.23 0.860 <0.001 0.65
 Bacteroidetes 27.93 23.56 5.03 12.08 5.34 11.41 5.20 2.53 1.63 4.74 3.50 0.410 <0.001 0.37
 Unclassified 4.66 3.44 12.20 12.53 8.60 6.16 4.36 4.17 5.08 4.03 1.70 0.380 <0.001 0.94
 Proteobacteria 7.42 6.54 0.03 0.00 0.03 0.06 0.00 0.23 0.00 0.00 1.00 0.880 <0.001 0.99
 Actinobacteria 0.05 0.07 3.10 2.27 3.38 1.30 0.09 0.90 0.08 0.18 1.10 0.560 0.040 0.66
 Tenericutes 0.03 0.18 0.05 0.26 0.36 0.08 0.02 0.11 0.12 0.05 0.10 0.740 0.400 0.07
 Synergistetes 0.43 0.47 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.11 0.920 <0.001 0.99
Family
 Streptococcaceae 0.54 1.61 1.08 5.23 0.21 5.48 41.16 47.85 52.04 58.19 6.84 0.270 <0.001 0.99
 Lactobacillaceae 1.50 13.10 20.43 20.42 39.05 29.74 17.15 21.54 4.87 10.85 7.12 0.560 <0.001 0.58
 Lachnospiraceae4 10.20 9.00 33.74 18.51 18.22 10.93 9.35 8.04 9.81 6.86 2.67 0.001 <0.001 0.10
 Ruminococcaceae 4.75 10.99**a 7.63 10.14a 6.75 7.64a 4.86 3.26b 4.09 3.32b 1.49 0.110 0.001 0.05
 Clostridiaceae 3.88 4.99a 1.27 3.68a 5.36 15.92***b 4.48 1.63a 10.74 5.40*a 2.30 0.400 0.001 0.001
 S24_7 6.20 4.41 3.64 7.76 2.73 10.34 2.60 0.92 0.46 4.01 2.74 0.160 0.210 0.28
 Erysipelotrichaceae 17.54 4.56 1.35 1.01 0.45 0.45 0.22 0.24 0.21 0.19 2.79 0.120 <0.001 0.06
 Bacteroidaceae 16.01 4.46 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.71 0.170 0.040 0.10
 Clostridiales spp. 7.83 8.69 5.59 5.98 2.47 4.53 3.29 1.80 5.37 3.26 1.49 0.950 <0.001 0.51
 Prevotellaceae 2.05 6.10 0.90 2.57 1.86 0.77 1.49 1.53 1.01 0.50 1.27 0.290 0.060 0.20
 unclassified bacteria 4.66 3.44 12.20 12.53 8.60 6.16 4.36 4.17 5.08 4.03 1.70 0.380 <0.001 0.94
 Erysipelotrichaceae 17.54 4.56 1.35 1.01 0.45 0.45 0.22 0.24 0.21 0.19 2.79 0.120 <0.001 0.06
 Enterobacteriaceae 6.96 5.97 0.03 0.00 0.02 0.06 0.00 0.23 0.00 0.00 1.41 0.860 <0.001 0.99
 Coprobacillaceae 0.02 0.02 1.05 0.60 2.44 0.31 4.77 1.99 1.96 0.06 1.58 0.140 0.210 0.87
 Bifidobacteriaceae 0.01 0.00 3.10 2.27 3.36 1.30 0.09 0.90 0.08 0.18 1.10 0.560 0.040 0.66
 Veillonellaceae 1.52 0.30a 0.45 1.14ab 2.06 0.51*a 1.65 3.15b 0.12 0.19a 0.62 0.780 <0.001 0.05
 Unclassified Firmicutes 2.36 1.90 0.91 1.89 0.83 0.81 0.79 0.25 0.62 0.50 0.39 0.900 <0.001 0.43
 Unclassified Bacteroidales 2.25 4.69 0.15 1.43 0.57 0.19 0.70 0.02 0.04 0.09 0.47 0.250 <0.001 0.17
Genus
 Streptococcus 0.54 1.59 1.07 5.21 0.21 5.47 41.11 47.79 51.98 58.11 6.84 0.270 <0.001 0.993
 Lactobacillus 1.50 13.08 20.43 20.41 39.04 29.72 17.14 21.54 4.86 10.85 7.12 0.564 <0.001 0.580
 Unclassified Lachnospiraceae5 10.12 8.96 31.56 17.64 16.59 9.61 8.34 7.28 8.72 5.96 2.54 0.002 <0.001 0.113
 unclassified Clostridiaceae 1.72 3.24a 0.89 3.41a 5.18 15.37***b 3.98 1.47a 10.10 5.02*ab 2.14 0.314 0.001 0.002
 Unclassified Clostridiales 7.83 8.69 5.59 5.98 2.47 4.53 3.29 1.80 5.37 3.26 1.49 0.950 0.001 0.512
 Unclassified Clostridia 6.17 6.32 4.63 3.14 2.97 2.73 1.76 1.44 2.01 1.23 0.95 0.357 <0.001 0.939
 Oscillospira 2.56 7.32***a 3.05 2.31b 1.70 2.47b 1.21 0.90b 1.05 1.17b 1.01 0.140 0.001 0.046
 p_75_a5 17.42 4.31** 0.84 0.23 0.05 0.03 0.00 0.00 0.03 0.03 2.76 0.110 0.001 0.050
 Faecalibacterium 0.01 0.02 1.91 2.78 2.27 0.60 1.81 1.48 0.59 0.40 0.05 0.390 <0.001 0.170
 Unclassified Ruminococcaceae 1.28 2.98** 1.26 1.22 0.75 1.28 0.69 0.27 1.09 0.67 0.45 0.330 0.004 0.074
 Sharpea 0.02 0.02 0.10 0.60 1.78 0.07 4.68 1.69 1.93 0.05 1.54 0.200 0.210 0.780
 Unclassified Firmicutes 2.36 1.90 0.91 1.89 0.83 0.81 0.79 0.25 0.62 0.50 0.39 0.900 <0.001 0.430
 Unclassified S24-7 6.20 4.41 3.64 7.76 2.73 10.34 2.60 0.92 0.46 4.01 2.74 0.163 0.218 0.279
 Bacteroides 15.65 4.29*** 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 3.79 0.171 <0.001 0.100
 Unclassified Bacteroidales 2.25 4.69 0.15 1.43 0.57 0.19 0.70 0.02 0.04 0.09 0.76 0.250 <0.001 0.171
 Escherichia 6.76 5.77 0.03 0.00 0.02 0.05 0.00 0.23 0.00 0.00 1.37 0.860 <0.001 0.990
 Bifidobacterium 0.01 0.00 3.10 2.27 3.36 1.30 0.09 0.90 0.08 0.18 1.10 0.560 0.038 0.663
 Unclassified bacteria 4.66 3.44 12.20 12.53 8.60 6.16 4.36 4.17 5.08 4.03 1.70 0.38 <0.001 0.940
Species (OTUs)
 C. saccharoperbutylacetonicum/beijerinckii (3) 1.53 3.05ac 0.46 3.01ac 4.96 15.07***b 3.82 1.36ac 9.82 4.83c 2.13 0.304 <0.001 0.003
 C. difficile (13) 1.05 2.09c 0.01 0.39ab 0.26 1.83*c 1.00 0.47a 3.06 1.68*bc 0.50 0.482 <0.001 0.01
 Ruminiclostridium thermocellum (30) 0.39 0.26a 0.63 2.31**b 0.28 1.81***b 0.25 0.06a 0.36 0.25a 0.29 0.002 <0.001 0.001
 E. rhusiopathiae (10) 16.08 3.93***a 0.78 0.22a 0.05 0.03a 0.00 0.00a 0.03 0.02a 2.57 0.110 <0.001 0.051
 L. reuteri (14) 0.11 1.14ab 0.47 4.01*b 5.76 3.28*b 1.03 0.14a 0.01 0.00a 0.95 0.681 <0.001 0.045
 M. elsdenii (25) 0.80 0.03ab 0.27 0.76ac 0.41 0.08a 0.49 1.70**c 0.03 0.11ab 0.34 0.514 0.015 0.024
 O. valericigenes (29) 0.83 2.88***a 0.24 0.18b 0.13 0.13b 0.19 0.11b 0.05 0.11b 0.44 0.147 <0.001 0.052
 Ruminococcaceae spp. (47) 0.20 0.02a 0.15 0.46*b 0.69 0.42*b 0.22 0.19a 0.33 0.16a 0.09 0.244 <0.001 0.047
 B. helcogenes (115) 0.00 0.00 0.03 0.08 0.05 0.01 0.32 0.02** 0.07 0.10 0.07 0.230 0.108 0.054
 Mitsuokella jalaludinii (122) 0.04 0.01a 0.01 0.00a 0.30 0.01***a 0.06 0.13b 0.00 0.00a 0.05 0.103 0.008 0.003
 L. delbrueckii subsp. bulgaricus (130) 0.04 0.00a 0.10 0.47***b 0.10 0.03a 0.04 0.02a 0.05 0.05a 0.04 0.024 <0.001 <0.001
 P. denticola (137 0.02 0.00a 0.00 1.55***b 0.01 0.03a 0.01 0.01a 0.00 0.00 0.16 0.003 0.000 <0.001
 E. harbinense (162) 0.02 0.01a 0.06 0.23***c 0.06 0.08b 0.02 0.02a 0.02 0.02a 0.01 <0.001 <0.001 <0.001
 S. suis (160) 0.00 0.00a 0.02 0.18***c 0.04 0.02a 0.05 0.03ab 0.06 0.03b 0.02 0.035 <0.001 <0.001
 R. albus (179) 0.00 0.00a 0.02 0.14***b 0.03 0.02a 0.04 0.02a 0.06 0.04a 0.02 0.254 0.006 0.01
 N. timonensis (84) 0.03 0.02a 0.03 0.37***b 0.34 0.39b 0.08 0.04a 0.11 0.03a 0.04 0.017 <0.001 <0.001

a-cPair-wise comparisons were made for SDPP treatment over time. Means without similar superscripts are different (P < 0.05).

1CTL: control. Control diet had no SDPP throughout the study.

2Pigs fed diet containing SDPP at 5% (d 0 to 14) and 2.5% (d 14 to 28).

3Treatment (trt) included CTL or SDPP.

4Treatment effect (P = 0.001; CTL = 16.3%; SDPP = 10.7%) when averaged across all timepoints.

5Treatment effect (P = 0.002; CTL = 15.1%; SDPP = 9.9%) when averaged across all timepoints.

*P < 0.05: SDPP compared with control at the corresponding timepoint.

**P < 0.01: SDPP compared with control at the corresponding timepoint.

***P < 0.001: SDPP compared with control at the corresponding timepoint.