TABLE 3

Association of individual ruminal liquid-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 liquids of high-RFI (less efficient) cows
    Anaerovibrio (100)0.3380.1730.0680.051
    Butyrivibrio (100)1.5910.8560.3010.050
    Clostridiales (100)0.2560.1560.0260.009
    Paraprevotellaceae (100)0.1460.0770.0310.069
    Prevotella (100)d0.1720.0490.0060.070
    Prevotella (100)0.2440.1420.0370.033
    Prevotella (100)2.6031.6690.4040.058
    Prevotella (100)0.4250.2400.0840.070
    Prevotella (100)0.2240.1000.0580.078
    Prevotellaceae (90)0.4840.2510.0880.038
    RF39 (100)0.1370.0820.0130.005
    Ruminococcaceae (100)0.1330.0710.0300.088
    Sharpea (100)1.0240.3380.2990.062
OTUs more abundant in ruminal liquids of low-RFI (more efficient) cows
    Clostridiales (100)0.0880.4180.1690.099
    Coprococcus (100)0.4240.7110.1120.059
    Lachnospiraceae (100)0.2070.4680.1260.082
    p-75-a5 in Erysipelotrichaceae (100)0.1110.1990.0360.051
    Prevotella (100)0.0470.5940.1970.032
    Prevotella (100)0.0770.5760.1900.039
    Prevotella (100)0.1120.2350.0470.039
    Prevotella (100)0.0700.8190.3130.054
    Prevotella (100)0.5320.9300.1700.058
    Prevotella (100)0.1290.2260.0440.070
    Prevotella (100)0.2741.5490.6520.099
    Pseudobutyrivibrio (100)0.0930.3370.1380.041
    RF39 (100)0.1830.3420.0800.092
    Shuttleworthia (100)0.2640.8270.2400.057
  • 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.