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Table 3 Effect of replacing soybean meal with dried distillers grains with solubles on relative abundance of major ruminal bacterial genera (each with a relative abundance ≥0.5% in at least one treatment) in different ruminal ecological niches of growing Hu lambs

From: Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs

Phylum Genus/other Protein source (PS) Ruminal ecological niche (REN) P-value
SBM DDGS SEM Solid Liquid Epithelial SEM PS REN PS× REN
Bacteroidetes Prevotella 1 19.19 19.50 2.779 25.01a 28.89a 3.94b 3.404 0.93 < 0.01 0.83
  Rikenellaceae RC9 gut group 7.09 5.76 0.589 6.59 7.13 5.57 0.721 0.12 0.31 0.39
  Prevotellaceae UCG-001 4.48 4.36 0.923 1.82b 1.23b 10.20a 1.131 0.93 < 0.01 0.93
  Bacteroidales S24-7 group 3.66 3.06 0.549 6.56a 2.42b 1.09b 0.672 0.45 < 0.01 0.25
  Bacteroidales BS11 gut group 2.81 2.61 0.655 2.18b 4.23a 1.72b 0.765 0.80 0.03 0.88
  Prevotellaceae Unclassified1 1.00 (3.79) 0.63 (0.36) 0.165 0.83 (1.54) 0.87 (3.97) 0.74 (0.72) 0.195 0.08 0.86 0.72
  Prevotellaceae UCG-003 1.73 1.13 0.347 1.61a 2.41a 0.28b 0.404 0.16 < 0.01 0.80
  Bacteroidetes Unclassified1 0.87 (1.24) 0.69 (0.48) 0.069 1.01a (1.39) 0.89a (1.07) 0.43b (0.11) 0.085 0.08 < 0.01 0.96
  Prevotellaceae NK3B31 group 0.51 1.33 0.551 2.29 0.39 0.09 0.675 0.30 0.06 0.62
  Bacteroidetes VC2.1 Bac22 0.49 0.31 0.136 0.72a 0.38ab 0.10b 0.150 0.18 < 0.01 0.41
  Bacteroidales RF16 group 0.71 0.62 0.212 0.12b 1.64a 0.25b 0.212 0.66 < 0.01 0.97
  Rikenellaceae U29-B031 0.53 (0.25) 0.60 (0.55) 0.062 0.46b (0.12) 0.38b (0.08) 0.84a (1.00) 0.077 0.43 < 0.01 0.33
  Rikenellaceae Blvii282     ND ND 1.402     
Firmicutes Christensenellaceae R-7 group1 1.86 (7.47) 2.01 (8.18) 0.111 1.99ab (8.25) 2.21a (11.79) 1.59b (3.43) 0.136 0.36 0.01 0.76
  Butyrivibrio 21 1.39 (5.95) 1.24 (5.18) 0.146 0.76b (0.57) 0.79b (0.61) 2.40a (15.51) 0.156 0.16 < 0.01 0.65
  Ruminococcaceae NK4A214 group 3.63 4.38 0.461 4.66a 5.95a 1.40b 0.564 0.25 < 0.01 0.39
  Succiniclasticum 1.99 1.39 0.270 2.60a 0.99b 1.48b 0.330 0.13 < 0.01 0.92
  Ruminococcus 1 0.92 0.94 0.201 2.04a 0.58b 0.17b 0.245 0.95 < 0.01 0.84
  Lachnospiraceae NK3A20 group 1.70 2.26 0.308 2.33 2.00 1.61 0.375 0.20 0.40 0.97
  Saccharofermentans 0.82 1.03 0.112 1.88a 0.75b 0.16c 0.137 0.18 < 0.01 0.38
  Ruminococcus 2 1.33 1.47 0.484 0.98b 3.11a 0.11b 0.559 0.80 < 0.01 0.76
  Eubacterium coprostanoligenes group 0.69 0.58 0.068 0.74b 1.08a 0.10c 0.082 0.25 < 0.01 0.13
  Ruminococcaceae UCG-014 0.91 1.08 0.112 1.10a 0.55b 1.33a 0.138 0.28 < 0.01 0.37
  Eubacterium ruminantium group 0.32 0.44 0.102 0.87a 0.19b 0.07b 0.113 0.24 < 0.01 0.48
  Lachnospiraceae XPB1014 group1 0.64 (0.60) 0.81 (1.08) 0.085 0.93a (1.35) 0.86a (1.10) 0.38b (0.07) 0.104 0.18 < 0.01 0.60
  Ruminococcaceae UCG-005 0.70 0.23 0.078 0.36 0.41 0.63 0.096 < 0.01 0.11 0.95
  Lachnospiraceae probable genus 10 0.24 0.34 0.093 0.694a 0.135b 0.046b 0.113 0.47 < 0.01 0.81
  Ruminococcaceae UCG-010 0.46 0.41 0.063 0.58a 0.45ab 0.29b 0.078 0.60 0.048 0.19
  Lachnospiraceae uncultured 0.30 0.38 0.108 0.63a 0.32ab 0.07b 0.125 0.56 < 0.01 0.79
  Family XIII AD3011 group 0.51 0.50 0.052 0.51 0.42 0.58 0.063 0.86 0.23 0.98
  Pseudobutyrivibrio3 0.44 1.06 0.135 0.56b 1.62a 0.06b 0.165 < 0.01 < 0.01 < 0.01
  Lachnospiraceae Unclassified1 0.73 (0.45) 0.83 (0.81) 0.097 0.82 (0.70) 0.74 (0.63) 0.77 (0.56) 0.105 0.23 0.69 0.39
  Lachnospiraceae AC2044 group1 0.48 (0.18) 0.54 (0.55) 0.074 0.199 0.73a (0.82) 0.44ab (0.20) 0.37b (0.07) 0.090 0.54 0.02 0.92
  Anaerovibrio 0.28 0.25 0.069 0.25ab 0.51a 0.03b 0.084 0.75 < 0.01 0.97
  Anaerovorax 0.26 0.45 0.102 0.27ab 0.13b 0.65a 0.102 0.20 0.02 0.24
  Lachnospiraceae UCG-0081 0.85 (1.34) 0.73 (0.65) 0.049 0.58b (0.21) 0.50b (0.13) 1.29a (2.65) 0.060 0.11 < 0.01 0.32
  Defluviitaleaceae UCG-011 0.30 0.25 0.089 0.16b 0.07b 0.59a 0.109 0.69 < 0.01 0.97
  Eubacterium nodatum group1 0.80 (1.10) 0.88 (1.45) 0.037 0.57b (0.20) 0.46b (0.11) 1.49a (3.52) 0.045 0.16 < 0.01 0.69
  Erysipelotrichaceae uncultured 0.38 0.42 0.068 0.20b 0.11b 0.89a 0.077 0.61 < 0.01 0.98
  Lachnospiraceae UCG-0101 0.37 (0.21) 0.36 (0.16) 0.034 0.15b (0.009) 0.16b (0.008) 0.78a (0.545) 0.042 0.86 < 0.01 0.32
  Howardella1 0.52 (0.43) 0.58 (0.61) 0.031 0.14c (0.004) 0.40b (0.071) 1.11a (1.49) 0.038 0.14 < 0.01 0.67
Proteobacteria Halomonas1 0.63 (0.56) 0.54 (0.50) 0.038 0.26b (0.03) 0.40b (0.07) 1.10a (1.49) 0.046 0.10 < 0.01 0.26
  Desulfobulbus1 0.64 (1.47) 0.74 (2.03) 0.056 0.13b (0.004) 0.28b (0.031) 1.66a (5.22) 0.069 0.24 < 0.01 0.39
  Comamonas1 0.35 (0.44) 0.36 (0.45) 0.057 0.03b (0.001) 0.07b (0.002) 0.96a (1.34) 0.098 0.91 < 0.01 0.97
  Suttonella1,3 0.42 (0.31) 0.28 (0.08) 0.028 0.06c (0.002) 0.22b (0.016) 0.76a (0.562) 0.034 < 0.01 < 0.01 < 0.01
  Neisseriaceae uncultured2     ND ND 2.66     
  Campylobacter2     ND ND 5.62     
Spirochaetes Treponema 2 2.90 3.05 0.851 2.44b 0.74b 5.74a 0.932 0.84 < 0.01 0.51
Fibrobacteres Fibrobacter 0.49 0.55 0.213 1.15a 0.11b 0.30b 0.235 0.83 < 0.01 0.94
  1. a-cMeans with different superscripts within a row of REN differ (P < 0.05)
  2. 1Data were cubic root transformed to ensure normality of residuals. Value in parenthesis is the mean of untransformed data in each treatment
  3. 2Genus/other can not be detected the rumen solid and liquid fraction, and only the difference of relative abundance of bacterial genera from rumen epithelium (RE) between SBM and DDGS (SBM-RE and DDGS-RE) was analyzed with SAS. Relative abundance (least square mean) of Blvii28, Neisseriaceae uncultured, and Campylobacter (%) for SBM-RE and DDGS-RE were 1.52 and 1.28 (P = 0.68); 2.52 and 2.80 (P = 0.88); 4.62 and 6.62 (P = 0.50), respectively
  4. 3Relative abundance (least square mean) of Pseudobutyrivibrio (%) was 0.52b, 0.74b, 0.07b, 0.61b, 2.52a and 0.06b for SBM-RS, SBM-RL, SBM-RE, DDGS-RS, DDGS-RL, and DDGS-RE, respectively, and that of Suttonella was 0.001b, 0.023b, 0.899a, 0.002b, 0.009b, and 0.225b for SBM-RS, SBM-RL, SBM-RE, DDGS-RS, DDGS-RL, and DDGS-RE, respectively. DDGS: dried distillers grains with solubles, SBM: soybean meal, RE: rumen epithelium, RS: rumen solid, RL: rumen liquid