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Table 2 The distribution of sequence reads, OTU's in absolute numbers and the ratio between Firmicutes and Bacteroides in pooled caecal samples

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

  Conventional cage Furnished cage Aviary
  Before inoculation 4 weeks PI Before inoculation 4 weeks PI Before inoculation 4 weeks PI
Number of reads 51,863 21,714 42,885 42,520 51,715 40,410
Number of OTU/total number of OTU 185/197 178/197 196/197 193/197 195/197 193/197
  93.9% 90.4% 99.5% 98.0% 99.0% 98.0%
Firmicutes/Bacteroides ratioa 0.81 0.61 0.87 0.74 0.69 0.68
  1. a The ratio was calculated by dividing all OTU that could be affiliated to Firmicutes (Clostridia and Bacilli) by the number of OTU's from Bacteroides.