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Table 1 Comparisons of T-RFLP profiles of microbiota in the ileum and caecum of layers housed in different cage systems

From: The influence of the cage system and colonisation of SalmonellaEnteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing

Before Inoculation
     Mean SD
Location Cage n T-RF Conventional Furnished Aviary
Ileum Conventional 4 10.5 ± 1.7 70.5 ± 12.4 - -
  Furnished 4 6.5 ± 2.7 67.4 ± 9.9 65.9 ± 7.5 -
  Aviary 4 7.3 ± 3.5 54.3 ± 9.6 66.8 ± 11.4 72.3 ± 7.0
Caecum Conventional 4 39.5 ± 6.6 66.4 ± 6.0 - -
  Furnished 4 39.8 ± 4.2 60.8 ± 3.5 75.1 ± 6.0 -
  Aviary 4 52.7 ± 23.5 38.6 ± 6.3 38.5 ± 4.8 45.4 ± 14.5
Four weeks PI
     Mean SD
Location Cage n T-RF Conventional Furnished Aviary
Ileum Conventional 8 10.0 ± 1.2 86.5 ± 10.1 - -
  Furnished 8 6.9 ± 2.2 65.5 ± 9.3 81.1 ± 6.9 -
  Aviary 7 10.7 ± 2.7 66.8 ± 9.2 67.5 ± 9.2 73.8 ± 9.0
Caecum Conventional 8 58.0 ± 5.2 73.4 ± 5.8 - -
  Furnished 8 51.3 ± 7.3 57.7 ± 8.1 67.1 ± 8.6 -
  Aviary 8 63.6 ± 5.3 54.6 ± 4.7 58.2 ± 4.9 74.2 ± 4.9
  1. n: number of samples
  2. SD: Dice similarity coefficient
  3. T-RF: Terminal Restriction Fragments
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