Table 2

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

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


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.

Nordentoft et al. BMC Microbiology 2011 11:187   doi:10.1186/1471-2180-11-187

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