Table 2 Microbial diversity and pathogen prevalence in 31 chicken samples determined using pyrosequencing

1

1

1

169

36.50

2.248

-

+

+

-

-

+

+

13

2

150

17.60

2.309

-

-

-

-

-

-

-

16

2

85

18.24

1.185

-

-

-

-

-

-

-

23

2

132

28.45

1.874

+

+

-

+

-

+

+

24

2

127

27.36

2.350

-

-

-

-

-

-

+

25

2

104

22.37

1.661

+

+

-

-

-

+

+

27

2

87

18.67

2.053

-

-

-

-

-

-

-

28

2

133

28.66

1.506

+

+

-

+

+

+

+

29

2

118

25.41

2.282

+

+

-

-

-

+

+

Average

123

24.81

1.940

Prevalence

44.4

55.6

11.1

22.2

11.1

55.6

66.7

2

4

1

97

20.85

2.049

+

+

-

+

-

+

+

6

1

113

24.82

2.970

+

+

-

-

-

+

-

8

1

200

43.21

2.701

+

+

-

-

+

+

+

9

1

139

29.97

2.987

+

-

-

-

-

+

+

10

1

23

4.78

2.490

-

-

-

-

-

-

-

17

2

102

21.93

2.413

-

+

-

-

-

+

+

20

2

71

15.20

1.659

-

-

-

-

-

-

-

21

2

107

23.02

1.598

-

+

-

-

+

+

+

26

2

92

19.76

2.434

-

+

-

-

+

+

+

31

2

162

34.96

2.632

+

+

+

-

-

+

+

Average

111

23.85

2.390

Prevalence

50.0

70.0

10.0

10.0

30.0

80.0

70.0

3

2

1

186

40.17

3.244

-

-

-

-

-

-

-

11

2

129

27.79

2.327

-

-

-

-

-

-

+

14

2

156

33.66

2.751

+

+

-

-

-

+

+

15

2

130

28.01

2.518

-

-

-

-

-

-

+

18

2

167

36.05

2.758

-

-

-

-

-

-

-

19

2

213

46.04

3.236

-

+

-

-

-

+

+

30

2

185

39.96

3.791

+

+

-

-

-

+

-

Average

167

35.95

2.950

Prevalence

28.6

42.9

0

0

0

42.9

57.1

4

3

1

91

19.54

2.570

+

+

-

-

-

+

-

5

1

112

24.10

2.830

+

+

-

-

+

+

-

7

1

140

30.18

3.059

-

+

-

-

+

+

-

12

2

150

32.35

3.015

-

+

-

-

+

+

-

22

2

46

9.77

2.835

-

-

-

-

-

-

-

Average

108

23.19

2.860

Prevalence

40.0

80.0

0

0

60.0

80.0

0

Total prevalence

41.9

61.3

6.4

9.7

22.6

64.5

54.8