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

From: The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens

Enterotype Sample Farm Species Species richness H’ Cjj Cjd Cco Cup Hpu Hbr Gal
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
  1. H’ is the Shannon index; Cjj is C. jejuni subsp. jejuni, Cjd is C. jejuni subsp. doylei; Cco is C. concisus; Cup is C. upsaliensis; Hpu is Helicobacter pullorum; Hbr is Helicobacter brantae; and Gal: Gallibacterium anatis.