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

BMC Microbiology

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 ratio^a	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.