Table 3

Listing of the most prevalent genera in caecal samples accounting for more than 1% of sequence in one or more samples

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


a) Percentages are presented as the relative distribution compared to all OTU's in the sample.

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

Open Data