Table 2 The most abundant (> 1%) archaeal and bacterial genera identified in metagenomics and metatranscriptomics data in cows treated with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12 weeks

Methanobrevibacter

82.36

75.27

70.38

2.28

73.89

66.96

69.74

2.39

0.02

< 0.001

< 0.001

0.55

< 0.001

Methanobacteriaceae

3.76

5.84

5.52

0.33

4.35

6.61

6.39

0.35

0.02

< 0.001

< 0.001

0.74

0.34

Methanosphaera

3.17

4.81

5.26

0.48

4.41

5.63

5.31

0.46

0.13

< 0.001

< 0.001

0.006

< 0.001

Methanobacterium

0.87

1.39

1.38

0.11

1.21

1.84

1.73

0.13

0.03

< 0.001

< 0.001

0.82

0.27

Methanosarcina

0.9

1.11

1.58

0.16

1.54

1.65

1.44

0.19

0.02

< 0.001

< 0.001

0.65

< 0.001

Thermoplasmata

0.79

1.04

1.3

0.17

1.01

1.59

1.56

0.16

0.01

< 0.001

< 0.001

0.82

< 0.001

Methanobrevibacter

78.6

72.19

69.46

1.66

74.01

67.18

66.82

1.84

0.12

< 0.001

< 0.001

< 0.001

< 0.001

Methanosphaera

6.14

9.65

11.07

0.88

7.32

10.68

7.92

0.81

0.76

< 0.001

< 0.001

0.002

< 0.001

Methanobacteriaceae

4.24

6.98

6.86

0.46

6.47

7.24

8.07

0.45

< 0.001

< 0.001

< 0.001

< 0.001

< 0.001

Thermoplasmata

4.83

4.14

4.51

0.39

5.13

6.82

8.03

0.8

0.17

< 0.001

< 0.001

< 0.001

< 0.001

Bacteroidetes Prevotella

16.19

16.14

18.56

0.826

17.54

16.52

14.66

0.81

0.24

< 0.001

< 0.001

< 0.001

< 0.001

Bacteria Unclassified

4.29

4.45

4.32

0.094

4.17

4.41

4.57

0.092

0.40

< 0.001

0.004

< 0.001

< 0.001

Fibrobacteres Fibrobacter

3.16

3.07

3.27

0.346

3.32

2.41

3.64

0.309

0.97

< 0.001

0.36

< 0.001

< 0.001

Firmicutes Butyrivibrio

3.6

3.33

2.72

0.332

2.72

2.85

3.18

0.209

0.006

< 0.001

< 0.001

< 0.001

< 0.001

Bacteroidetes Bacteroides

2.55

2.52

2.75

0.092

3

2.75

2.54

0.094

0.002

0.66

< 0.001

< 0.001

< 0.001

Firmicutes Lachnospiraceae

2.06

2.13

1.94

0.068

1.97

2.02

2.07

0.03

0.007

< 0.001

< 0.001

0.42

< 0.001

Firmicutes Clostridium

1.86

1.98

1.87

0.041

1.74

2.03

1.98

0.061

0.02

< 0.001

0.38

< 0.001

< 0.001

Actinobacteria Bifidobacterium

2.24

2.13

1.45

0.471

2.1

1.93

1.4

0.323

0.82

< 0.001

< 0.001

0.001

< 0.001

Firmicutes Lachnoclostridium

1.51

1.64

1.45

0.052

1.49

1.56

1.59

0.026

0.10

< 0.001

< 0.001

0.002

< 0.001

Firmicutes Clostridia

1.38

1.47

1.33

0.045

1.27

1.42

1.5

0.053

0.19

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Ruminococcus

1.38

1.35

1.29

0.071

1.05

1.31

1.27

0.07

< 0.001

< 0.001

< 0.001

< 0.001

< 0.001

Actinobacteria Olsenella

1.1

1.16

1.4

0.137

1.25

1.15

1.16

0.114

0.38

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Clostridiales

1.14

1.16

1.07

0.036

1.1

1.13

1.2

0.044

0.41

0.09

< 0.001

< 0.001

< 0.001

Bacteroidetes Prevotellaceae

0.89

0.96

1.11

0.069

1.11

1.05

0.88

0.059

0.01

< 0.001

< 0.001

< 0.001

< 0.001

Bacteroidetes Prevotella

17.65

16.96

18.74

0.749

16.1

16.42

14.9

0.559

0.26

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Lachnospiraceae

3.81

4.16

3.9

0.144

4.39

4.05

4.62

0.15

0.20

< 0.001

< 0.001

< 0.001

< 0.001

Bacteria

3.74

3.68

3.61

0.07

3.63

3.58

3.77

0.056

0.71

< 0.001

0.56

0.001

< 0.001

Fibrobacteres Fibrobacter

3.77

3.65

3.92

0.425

3.15

2.8

3.22

0.269

0.21

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Ruminococcus

3.47

3.71

3.05

0.218

2.59

2.83

2.86

0.145

0.16

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Butyrivibrio

3.17

2.98

2.77

0.218

3

2.95

2.9

0.195

0.52

0.002

< 0.001

< 0.001

< 0.001

Firmicutes Lachnoclostridium

1.97

2.13

1.99

0.068

2.28

2.05

2.53

0.1

0.005

< 0.001

< 0.001

< 0.001

< 0.001

Bacteroidetes Bacteroides

2.01

1.87

1.96

0.074

2.04

1.92

1.74

0.069

0.98

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Clostridium

1.24

1.47

1.71

0.199

2.5

1.56

1.96

0.259

< 0.001

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Eubacterium

1.51

1.72

1.6

0.073

2.06

1.68

1.71

0.111

0.10

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Clostridia

1.54

1.54

1.41

0.065

1.61

1.49

1.79

0.075

0.51

< 0.001

0.65

< 0.001

< 0.001

Firmicutes Clostridiales

1.34

1.36

1.28

0.05

1.4

1.36

1.6

0.06

0.42

< 0.001

< 0.001

< 0.001

< 0.001

Actinobacteria Olsenella

1.12

1.15

1.49

0.116

0.94

1.27

1.53

0.129

0.34

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Faecalibacterium

1.24

1.24

1.16

0.036

1.16

1.21

1.38

0.04

0.92

< 0.001

< 0.001

< 0.001

< 0.001

Actinobacteria Bifidobacterium

1.34

1.57

0.77

0.407

1.72

0.78

1.11

0.17

0.45

< 0.001

< 0.001

< 0.001

< 0.001

Proteobacteria Proteobacteria

1.3

1.2

1.19

0.045

1.1

1.21

1.1

0.056

0.003

< 0.001

< 0.001

< 0.001

< 0.001

Bacteroidetes Prevotellaceae

1.12

1.24

1.4

0.11

1.12

1.17

1.04

0.06

0.65

< 0.001

< 0.001

< 0.001

< 0.001

Firmicutes Megasphaera

0.27

0.3

1.08

0.29

0.23

3.83

0.3

1.302

0.92

< 0.001

< 0.001

< 0.001

< 0.001