Figure 1.
(A) Rarefaction curves of the OTUs clustered at 97% sequence identity for each chicken, based on the averages of the four replicates per bird. (B) Hierarchical clustering visualizing similarities among cecal samples. The number in each label indicates each individual chicken and the letter each individual ceca (either A or B). Technical replicates of each ceca were carried out. (C) Bar chart showing the proportion of reads assigned to the top 5 most abundant OTUs in each chicken.
Table 1.
Draft genome sequences recovered from the chicken cecal metagenome.
Figure 2.
Polysaccharide-degrading enzymes in the chicken cecal metagenome.
The figure shows each class of enzyme as judged by SEED/KEGG annotation and GH (see methods) for three types of NSP. The size of pie chart reflects abundance of the enzyme class; numbers indicate quantity of genes assigned to each bacterial Taxon at the class level.
Table 2.
Number of genes containing GH domains in different metagenomes.
Figure 3.
Gene clusters associated with polysaccharide degradation and utilization.
NSP degrading genes were identified by SEED/KEGG annotation and GH domain (see methods). (A) Gene clusters encoding putative PUL systems from various Bacteroidetes. (B) Gene cluster encoding putative integrated polysaccharide degradation and utilization systems from various Firmicutes. (C) NSP degrading enzymes associated with sporulation genes * indicates predicted signal peptide.
Figure 4.
Pathways and gene clusters associated with propionoate production in the chicken cecal metagenome.
(A) Pathways involved in propionoate production showing the putative genes identified coding for the enzymes involved. Size of pie chart reflects abundance of the gene class; numbers indicate quantity of genes assigned to each taxon. (B) Operon structure of two Methylmalonyl decarboxylase loci.
Figure 5.
Pathways and gene clusters associated with butyrate production in the chicken cecal metagenome.
(A) Pathways involved in butyrate production showing the putative genes identified coding for the enzymes involved. Size of pie chart reflects abundance of the gene class; numbers indicate quantity of genes assigned to each taxon. (B) Operon structure of two butyryl-CoA:acetate-CoA transferase (BCD) loci.
Figure 6.
Potential Hydrogen sinks in the Chicken cecal metagenome.
The key genes involved in each pathway that could potentially use hydrogen are shown. The size of pie chart reflects abundance of the gene class; numbers indicate quantity of genes assigned to each taxon.