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Table 3 Listing of the most prevalent genera in caecal samples accounting for more than 1% of sequence in one or more 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 Furnished Aviary
Class Family Genus Before inoculation (%)a 4 Weeks PI (%) Before inoculation (%) 4 Weeks PI (%) Before inoculation (%) 4 Weeks PI (%)
Bacteroidia Rikenellaceae Alistipes 2.3 1.1 1.4 1.7 1.4 1.2
  Bacteroides Bacteroides 1.4 1.4 5.3 4.8 6.2 5.6
  Bacteroidaceae Bacteroides 2.1 2.5 0.7 2.1 1.7 2.6
  Porphyromonadaceae Barnesiella 1.2 3.1 1.1 2.0 2.3 1.4
  Porphyromonadaceae Butyricimonas 28.8 20.6 12.4 14.7 13.8 18.8
  Porphyromonadaceae Parabacteroides 2.8 4.4 4.9 5.4 4.6 3.8
   Unclas. Bacteroidales 4.4 9.8 9.0 7.1 10.3 8.9
   Unclas. Bacteroidales 0.7 2.6 2.1 3.0 4.9 2.5
   Unclas. Bacteroidales 0.2 2.0 1.0 2.5 1.0 1.9
   total for class 43.8 47.4 37.8 43.1 46.2 46.6
Clostridia Clostridiales Blautia 0.6 0.4 1.3 0.5 1.1 0.4
  Ruminococcaceae Faecalibacterium 18.6 11.6 13.6 19.0 16.7 13.9
  Veillonellaceae Phascolarctobacterium 4.3 0.9 2.6 0.4 1.8 3.8
  Ruminococcaceae Subdoligranulum 0.0 0.2 1.4 1.6 0.9 0.4
   total for class 23.6 21.0 19.0 22.0 20.0 23.0
Bacilli Lactobacillaceae Lactobacillus 3.8 0.4 0.3 0.1 0.2 0.1
  Lactobacillaceae Lactobacillus 2.3 4.8 5.4 2.5 1.9 5.0
   total for class 6.1 5.3 5.7 2.5 2.1 5.1
Betaproteobacteria Alcaligenaceae Sutterella 1.5 1.1 0.5 0.7 0.3 0.6
  Alcaligenaceae Sutterella 1.1 0.8 0.6 0.9 0.6 0.8
   total for class 2.6 1.9 1.1 1.6 0.9 1.4
Fusobacteria Fusobacteriaceae Fusobacterium 2.2 1.3 2.4 1.5 1.8 0.1
Actinobacteria Coriobacteriaceae Olsenella 1.7 3.9 1.8 1.4 0.4 1.9
Deferribacteres Deferribacteraceae Mucispirillum 0.9 1.7 2.0 1.8 1.5 1.9
Epsilonproteobacteria Helicobacteraceae Helicobacter 0.5 0.6 3.6 0.6 0.5 0.8
Synergistia Synergistaceae Cloacibacillus 0.9 2.0 1.1 1.0 1.3 1.0
Alphaproteobacteria   Unclas. Alphaproteobacteria 0.2 0.1 1.6 0.5 0.3 0.4
Unclas. Bacteria   Unclas. Bacteria 0.2 0.6 2.6 2.0 2.0 1.5
Unclas. Firmicutes   Unclas. Firmicutes 1.1 0.7 0.6 1.1 1.1 0.6
  1. a) Percentages are presented as the relative distribution compared to all OTU's in the sample.