TABLE 4

Association of individual ruminal solid phase OTUs with relative RFI by a reduced mixed model of relative sequence abundance

OTU taxonomy (confidence)aHigh RFI LSMbLow RFI LSMSEDcP > Fd
OTUs more abundant in ruminal solids of high-RFI (less efficient) cows
    Anaerovibrio (100)0.2720.1430.0560.061
    Butyrivibrio (100)3.0911.6940.3440.007
    CF231 in Paraprevotellaceae (100)0.4460.2290.0590.010
    Clostridia (100)0.5440.2440.1250.041
    Clostridiales (100)0.6700.4150.1160.070
    Clostridium (100)0.3180.2000.0520.064
    F16 in TM7 (100)0.1260.0860.0190.085
    Lachnospiraceae (90)0.1020.0510.0210.047
    Lachnospiraceae (100)0.5420.2290.0860.011
    Lachnospiraceae (100)0.1240.0660.0170.015
    Lachnospiraceae (100)1.0220.5680.1670.035
    Lachnospiraceae (100)0.3200.1520.0780.073
    Lachnospiraceae (99)0.2020.0860.0350.016
    Prevotella (100)0.1430.0790.0220.029
    Prevotella (100)0.3630.2280.0510.038
    Prevotella (100)2.9661.8660.4940.068
    Prevotella (100)1.3211.1060.1540.096
    Pseudobutyrivibrio (100)1.5070.9100.1830.017
    Ruminococcaceae (81)0.9900.7400.1090.061
    Ruminococcus (100)0.5160.1970.1380.060
    S24-7 in Bacteroidales (100)0.5690.9000.1440.062
    Succinivibrio (97)0.3890.1690.0800.033
    YRC22 in Paraprevotellaceae (100)0.2900.2150.0120.001
OTUs more abundant in ruminal solids of low-RFI (more efficient) cows
    Butyrivibrio (97)0.0380.1100.0280.041
    Clostridiales (100)0.0950.2200.0430.027
    Clostridiales (100)0.1600.2580.0440.067
    Clostridiales (100)0.0050.2410.1140.084
    Lachnospiraceae (100)0.0671.3440.4690.035
    Lachnospiraceae (100)0.1200.1740.0300.036
    Lachnospiraceae (100)0.0820.1580.0390.096
    Prevotella (100)0.0710.2120.0370.009
    Prevotella (100)1.2611.5870.1010.018
    Prevotella (100)0.0800.1690.0290.023
    Prevotella (100)0.2810.4540.0580.024
    Prevotella (100)0.0000.0880.0300.028
    Prevotella (100)0.2360.4520.0810.038
    Prevotella (100)0.00250.1930.0730.041
    Prevotella (100)0.0250.3590.1490.066
    Prevotella (100)0.0380.1970.0730.072
    Prevotella (100)0.0200.1380.0540.073
    Prevotella (100)0.1730.4120.1160.085
    Prevotella (100)0.0050.4080.2010.092
    Shuttleworthia (100)0.0020.1250.0600.085
    Veillonellaceae (100)0.0270.1050.0370.079
  • a Statistical comparisons were made only those on those OTUs whose average across all cows exceeded 0.1% of reads. Taxonomy for each OTU is given at the highest classifiable level, with the classification confidence in parentheses. Each listed OTU taxonomy represents a unique OTU for the indicated taxon (e.g., multiple entries for Prevotella represent different OTUs within that genus).

  • b LSM, least square mean of relative abundance (expressed as percentage of total sequence reads).

  • c SED, standard error of the difference between means.

  • d P > F, probability of obtaining a higher F-test value from the model.