Table 1 Results of permutational multivariate analysis of variance (PERMANOVA) based on Euclidean distances for phage counts of 52 ssRNA phage contigs detected in metatranscriptome data from (A) Trial 1 and (B) Trial 2.

From: The dynamics of single stranded, positive sense RNA bacteriophages in the rumen virome

 

Df

Sum Sq

R2

F value

Pr(> F)

(A) Trial 1

 Timeseries 1A

  Experimental day

3

107.30

0.199

0.90

0.0007

  Diet

3

78.59

0.146

0.66

0.3719

  Residual

9

357.26

0.662

  

  CowID

3

245.95

0.455

3.35

0.0003

  Residual

12

294.05

0.545

  

(B) Trial 2

 Timeseries 2A

  Experimental day

1

102.97

0.088

2.38

0.0004

  Diet

1

120.78

0.103

2.79

0.0001

  Residual

20

864.95

0.737

  

  Cow ID

7

367.08

0.313

1.04

0.3334

  Residual

16

805.92

0.687

  

 Timeseries 2B

  Sampling time

2

7.28

0.003

0.09

0.9995

 Experimental day

1

277.88

0.116

6.70

0.0001

  Diet

1

321.33

0.135

7.75

0.0001

  Residual

43

1782.65

0.746

  

  Cow ID

7

998.97

0.418

4.11

0.0001

  Residual

40

1390.17

0.582

  

 Baseline dataset

  SampleType

2

28.23

0.026

0.28

0.0020

  Residual

21

1075.77

0.974

  

  CowID

7

959.82

0.869

15.22

0.0001

  Residual

16

144.18

0.131

  
  1. PERMANOVA was conducted to evaluated changes in phage composition over time (within 5 h: Timeseries 2B; weekly: Timeseries 1A; every third week after diet shift: Timeseries 2A) and differences between rumen fractions (Baseline dataset), restricting permutations within cow accounting for repeated measurements (Model 1). Cow-specific effects on ssRNA phage composition were assessed for each dataset, separately (Model 2). Results include degrees of freedom (Df), sum of squares, proportion of variation explained (R2), pseudo-F statistics, and P values obtained from 9999 permutations.
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