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Table 4 Comparisons of alpha-diversity indices1 between beef cattle with different RFI values

From: Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

  Angus (n = 16) Charolais (n = 16) (mean ± SEM) Kinsella composite hybrid (n = 16)
Bacteria
 Chao1
  L-RFI 317.03 ± 11.83 319.87 ± 12.95 381.88 ± 37.60
  H-RFI 337.64 ± 21.82 326.69 ± 16.70 358.74 ± 27.93
  P value2 NS NS NS
 Shannon evenness
  L-RFI 0.57 ± 0.01 0.59 ± 0.01 0.57 ± 0.01
  H-RFI 0.58 ± 0.01 0.55 ± 0.02 0.54 ± 0.01
  P value2 NS 0.03 NS
 Simpson evenness
  L-RFI 0.05 ± 0.00 0.05 ± 0.01 0.05 ± 0.00
  H-RFI 0.05 ± 0.00 0.04 ± 0.00 0.04 ± 0.00
  P value2 NS NS NS
 Shannon index
  L-RFI 3.17 ± 0.05 3.28 ± 0.06 3.21 ± 0.04
  H-RFI 3.18 ± 0.06 3.06 ± 0.10 3.01 ± 0.07
  P value2 NS NS 0.04
 Inverse Simpson
  L-RFI 12.26 ± 0.96 13.89 ± 1.22 13.18 ± 0.74
  H-RFI 12.78 ± 0.97 10.96 ± 1.31 10.53 ± 1.14
  P value2 NS NS NS
Archaea
 Chao1
  L-RFI 25.88 ± 1.03 28.06 ± 2.36 24.17 ± 0.95
  H-RFI 24.25 ± 1.22 24.65 ± 1.38 25.31 ± 1.32
  P value2 NS NS NS
 Shannon evenness
  L-RFI 0.64 ± 0.02 0.62 ± 0.02 0.66 ± 0.02
  H-RFI 0.64 ± 0.02 0.66 ± 0.01 0.65 ± 0.01
  P value2 NS NS NS
 Simpson evenness
  L-RFI 0.22 ± 0.02 0.20 ± 0.01 0.24 ± 0.02
  H-RFI 0.23 ± 0.02 0.26 ± 0.02 0.24 ± 0.01
  P value2 NS 0.03 NS
 Shannon index
  L-RFI 2.00 ± 0.07 1.95 ± 0.06 2.07 ± 0.07
  H-RFI 1.98 ± 0.07 2.07 ± 0.04 2.05 ± 0.03
  P value2 NS NS NA
 Inverse Simpson
  L-RFI 5.21 ± 0.51 4.74 ± 0.37 5.67 ± 0.46
  H-RFI 5.19 ± 0.50 5.93 ± 0.36 5.48 ± 0.14
  P value2 NS 0.03 NS
  1. NS not significant with P value not less than 0.05
  2. 1To make alpha-diversity indices comparable among samples, the number of sequences per sample was normalized to the lowest reads number for bacteria (n = 274,885) and archaea (n = 4263), respectively
  3. 2P values were obtained between H- and L-RFI groups within each breed using the Kruskal-Wallis rank-sum test