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Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits

View Article: PubMed Central - PubMed

ABSTRACT

Our study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus). Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups. Four Cluster of Orthologous Group (COG) categories (Amino acid transport and metabolism, E; Nucleotide transport and metabolism, F; Coenzyme transport and metabolism, H; and Lipid transport and metabolism, I) were overrepresented in LL samples. Fifteen differential metabolic pathways (Biosynthesis of amino acids, Pyruvate metabolism, Nitrotoluene degradation, Lipopolysaccharide biosynthesis, Peptidoglycan biosynthesis, Pantothenate and CoA biosynthesis, Glycosaminoglycan degradation, Thiamine metabolism, Phosphotransferase system, Two-component system, Bacterial secretion system, Flagellar assembly, Bacterial chemotaxis, Ribosome, Sulfur relay system) were identified. Our data highlighted interesting variations between the gut metagenomes of these two chicken lines.

No MeSH data available.


Comparison of the structure of lean and fat chicken gut metagenomes.(A) Differential abundance of COG functional categories of the two chicken lines. COG category codes are as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; W, Extracellular structures; Y, Nuclear structure; Z, Cytoskeleton. P-values of <0.01 and <0.05 are represented by ‘**’ and ‘*’, respectively.
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f5: Comparison of the structure of lean and fat chicken gut metagenomes.(A) Differential abundance of COG functional categories of the two chicken lines. COG category codes are as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; W, Extracellular structures; Y, Nuclear structure; Z, Cytoskeleton. P-values of <0.01 and <0.05 are represented by ‘**’ and ‘*’, respectively.

Mentions: The structure and function of the LL and FL gut microbial metagenome were analyzed based on the COG and KEGG functions. The relative abundances of all the COG functional groups in the LL and FL chickens are represented by box plots (Fig. 5). Four of the functional categories were significantly different between the two chicken lines (all with relative abundance of lean > fat line), which were Amino acid transport and metabolism (E) (p = 0.0350), Nucleotide transport and metabolism (F) (p = 0.0042), Coenzyme transport and metabolism (H) (p = 0.0186), and Lipid transport and metabolism (I) (p = 0.0079), respectively. To visualize the functional difference between the two sample groups, PCA analysis was performed based on all detected KO (Fig. 6A) (with PC1 and PC2 representing 57.01% and 18.03% of the total variance). Although only a weak clustering pattern was observed on the score plot with mild overlap of symbols representing the two groups, further analysis by MANOVA revealed that they were significantly different (p = 0.0012) (Fig. 6B).


Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
Comparison of the structure of lean and fat chicken gut metagenomes.(A) Differential abundance of COG functional categories of the two chicken lines. COG category codes are as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; W, Extracellular structures; Y, Nuclear structure; Z, Cytoskeleton. P-values of <0.01 and <0.05 are represented by ‘**’ and ‘*’, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120256&req=5

f5: Comparison of the structure of lean and fat chicken gut metagenomes.(A) Differential abundance of COG functional categories of the two chicken lines. COG category codes are as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; W, Extracellular structures; Y, Nuclear structure; Z, Cytoskeleton. P-values of <0.01 and <0.05 are represented by ‘**’ and ‘*’, respectively.
Mentions: The structure and function of the LL and FL gut microbial metagenome were analyzed based on the COG and KEGG functions. The relative abundances of all the COG functional groups in the LL and FL chickens are represented by box plots (Fig. 5). Four of the functional categories were significantly different between the two chicken lines (all with relative abundance of lean > fat line), which were Amino acid transport and metabolism (E) (p = 0.0350), Nucleotide transport and metabolism (F) (p = 0.0042), Coenzyme transport and metabolism (H) (p = 0.0186), and Lipid transport and metabolism (I) (p = 0.0079), respectively. To visualize the functional difference between the two sample groups, PCA analysis was performed based on all detected KO (Fig. 6A) (with PC1 and PC2 representing 57.01% and 18.03% of the total variance). Although only a weak clustering pattern was observed on the score plot with mild overlap of symbols representing the two groups, further analysis by MANOVA revealed that they were significantly different (p = 0.0012) (Fig. 6B).

View Article: PubMed Central - PubMed

ABSTRACT

Our study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus). Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups. Four Cluster of Orthologous Group (COG) categories (Amino acid transport and metabolism, E; Nucleotide transport and metabolism, F; Coenzyme transport and metabolism, H; and Lipid transport and metabolism, I) were overrepresented in LL samples. Fifteen differential metabolic pathways (Biosynthesis of amino acids, Pyruvate metabolism, Nitrotoluene degradation, Lipopolysaccharide biosynthesis, Peptidoglycan biosynthesis, Pantothenate and CoA biosynthesis, Glycosaminoglycan degradation, Thiamine metabolism, Phosphotransferase system, Two-component system, Bacterial secretion system, Flagellar assembly, Bacterial chemotaxis, Ribosome, Sulfur relay system) were identified. Our data highlighted interesting variations between the gut metagenomes of these two chicken lines.

No MeSH data available.