Table 6 Genus-level differences in the caecal microbiota between A. suum single-infected (SI), trickle-infected (TI) and non-infected (C) pigs

Day 21 p.i.

 Gemmiger (Ruminococcaceae)

4.65 ± 1.69

7.53 ± 1.3

0.57 ± 1.25

11.24

2

0.038

0.138

0.002

 Prevotella (Prevotellaceae)

26.19 ± 14.44

10.66 ± 7.28

3.52 ± 5.58

9.24

2

0.049

0.005

0.229

Megasphaera (Veillonellaceae)

2.93 ± 2.22

2.24 ± 1.37

0.11 ± 0.28

10.52

2

0.038

0.012

0.012

Faecalibacterium (Ruminococcaceae)

3.02 ± 0.84

6.02 ± 1.68

0.57 ± 0.89

11.78

2

0.038

0.101

0.001

 Romboutsia (Peptostreptococcaceae)

0.17 ± 0.11

0.41 ± 0.14

7.37 ± 10.76

11.13

2

0.038

0.002

0.132

 Blautia (Lachnospiraceae)

2.39 ± 0.9

2.58 ± 0.78

0.3 ± 0.56

9.57

2

0.047

0.026

0.012

 Fusicatenibacter (Lachnospiraceae)

0.27 ± 0.12

0.27 ± 0.14

0.03 ± 0.07

9.41

2

0.048

0.017

0.020

 Collinsella (Coriobacteriaceae)

0.54 ± 0.38

0.2 ± 0.15

0.03 ± 0.06

10.37

2

0.038

0.003

0.129

 Holdemanella (Erysipelotrichaceae)

0.22 ± 0.08

0.35 ± 0.23

0.02 ± 0.05

10.33

2

0.038

0.035

0.006

 Olsenella (Coriobacteriaceae)

0.14 ± 0.08

0.23 ± 0.13

0.02 ± 0.04

9.40

2

0.048

0.069

0.007

 Peptococcus (Peptococcaceae 1)

0.08 ± 0.11

0.07 ± 0.02

0.00 ± 0.00

9.38

2

0.048

0.074

0.007

 Acidaminococcus (Acidaminococcaceae)

0.22 ± 0.31

0.00 ± 0.00

0 ± 0.01

11.89

2

0.038

0.007

0.893

Day 35 p.i.

 Gemmiger (Ruminococcaceae)

0.00 ± 0.00

2.60 ± 1.1

4.13 ± 1.57

11.95

2

0.038

0.002

0.575

 Prevotella (Prevotellaceae)

0.06 ± 0.16

18.06 ± 4.57

9.69 ± 7.82

11.93

2

0.038

0.041

0.491

 Megasphaera (Veillonellaceae)

0.00 ± 0.00

0.32 ± 0.58

3.90 ± 3.73

10.50

2

0.038

0.003

0.074

 Roseburia (Lachnospiraceae)

0.01 ± 0.02

3.59 ± 1.51

3.02 ± 2.05

10.95

2

0.038

0.013

0.970

 Unknown Lachnospiraceae

0.00 ± 0.00

4.25 ± 2.26

5.41 ± 1.29

11.28

2

0.038

0.005

0.918

 Butyricicoccus (Clostridiaceae)

0.00 ± 0.00

0.30 ± 0.36

2.77 ± 1.26

12.57

2

0.038

< 0.001

0.051

 Faecalibacterium (Ruminococcaceae)

0.00 ± 0.00

0.63 ± 0.75

3.21 ± 1.61

12.60

2

0.038

< 0.001

0.127

 Lachnospiracea inc. sed. (Lachnospiraceae)

0.01 ± 0.02

1.80 ± 0.61

2.07 ± 1.53

10.95

2

0.038

0.013

0.970

 Phascolarctobacterium (Acidaminococcaceae)

0.00 ± 0.00

1.36 ± 0.92

0.94 ± 0.78

11.28

2

0.038

0.014

0.918

 Blautia (Lachnospiraceae)

0.00 ± 0.00

1.01 ± 0.62

1.76 ± 0.44

11.71

2

0.038

0.001

0.217

 Coprococcus (Lachnospiraceae)

0.00 ± 0.00

1.03 ± 0.63

1.88 ± 1.22

10.58

2

0.038

0.003

0.430

 Dorea (Lachnospiraceae)

0.00 ± 0.00

0.13 ± 0.1

0.56 ± 0.07

13.16

2

0.038

< 0.001

0.093

 Unknown Erysipelotrichales

0.00 ± 0.00

1.16 ± 1.46

0.6 ± 0.51

13.14

2

0.038

< 0.001

0.094

 Unknown Bacteroidia

0.00 ± 0.00

1.16 ± 1.46

0.60 ± 0.51

9.35

2

0.048

0.017

1.000

 Unknown Clostridiales

0.03 ± 0.06

1.70 ± 2.1

1.68 ± 0.92

9.72

2

0.046

0.007

0.769

 Oribacterium (Lachnospiraceae)

0.00 ± 0.00

0.14 ± 0.19

0.5 ± 0.34

9.92

2

0.043

0.003

0.102

 Fusicatenibacter (Lachnospiraceae)

0.00 ± 0.00

0.05 ± 0.11

0.26 ± 0.22

9.95

2

0.043

0.004

0.049

 Ruminococcus 2 (Ruminococcaceae)

0.00 ± 0.00

0.04 ± 0.08

0.38 ± 0.25

12.19

2

0.038

0.002

0.014

 Collinsella (Coriobacteriaceae)

0.00 ± 0.00

0.01 ± 0.02

0.29 ± 0.16

13.03

2

0.038

0.001

0.009

 Unknown Prevotellaceae

0.00 ± 0.00

0.69 ± 0.5

0.37 ± 0.24

11.48

2

0.038

0.019

0.805

 Holdemanella (Erysipelotrichaceae)

0.00 ± 0.00

0.00 ± 0.00

0.28 ± 0.15

14.41

2

0.038

0.001

0.002

 Unknown Firmicutes

0.00 ± 0.00

0.08 ± 0.07

0.26 ± 0.22

10.58

2

0.038

0.003

0.430

 Selenomonas (Selenomonadaceae)

0.00 ± 0.00

0.41 ± 0.55

0.23 ± 0.18

11.30

2

0.038

0.014

0.918

 Anaerovibrio (Veillonellaceae)

0.00 ± 0.00

0.48 ± 0.28

0.22 ± 0.29

11.95

2

0.038

0.032

0.575

 Paraeggerthella (Coriobacteriaceae)

0.00 ± 0.00

0.03 ± 0.04

0.11 ± 0.05

10.82

2

0.038

0.002

0.062

 Unknown Coriobacteriaceae

0.00 ± 0.00

0.13 ± 0.13

0.28 ± 0.18

11.10

2

0.038

0.002

0.312