Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks

Abstract

In this study, we sought to determine the effects of intestinal flora on the feed efficiency of meat ducks by evaluating the correlation between intestinal flora and residual feed intake. The F₂ generation of Cherry Valley ducks × Runzhou Crested White ducks was used as the study subjects, and feed consumption being recorded from d 21 to 42. RFI was calculated based on growth performance, and 20 low RFI and 20 high RFI ducks were randomly selected to characterize the effect of RFI on growth performance. To analyze the intestinal flora affecting RFI, 16s rDNA sequencing was performed on the contents of 5 intestinal segments from the HR and LR groups, and macrogenomic sequencing was performed on the cecal contents. Feed intake, average daily feed intake, feed conversion ratio, and residual feed intake were lower in low RFI. Analysis of the intestinal flora revealed the cecum to be more highly enriched in the carbohydrate metabolism pathway and less enriched with potentially pathogenic taxa than the other assessed intestinal regions. Further analysis of the cecal microbiota identified nine significantly differentially enriched intestinal flora. In this study, we accordingly identified a basis for the mechanisms underlying the effects of the intestinal flora on meat duck feed efficiency.

Keywords: 16s rDNA; intestinal flora; meat duck; metagenome; residual feed intake.

Figure 1

Analysis of the operational taxonomic units and α diversity of the gut microbiota in ducks. (A–E) Wayne plots of operational taxonomic units (OTUs) in the duodenum, jejunum, ileum, cecum, and rectum of ducks in the high and low RFI groups. (F and G) α-diversity analyses based on the Chao1 and Shannon indices, respectively.

Figure 2

Stacked maps of the distribution of the gut microbiota in duck intestines. (A–F) Distribution of bacteria at the phylum, class, order, family, genus, and species levels, respectively.

Figure 3

Network plots showing the Pearson correlations among different bacterial taxa. (A–F) Correlations for bacteria at the phylum, class, order, family, genus, and species levels, respectively The size of the dots corresponds to taxon abundance, a solid red line indicates a positive correlation, and a blue dotted line indicates a negative correlation.

Figure 4

Box plots of Wilcoxon rank-sum analyses of the abundances of bacterial taxa in different duck intestinal segments. (A–E) duodenum, jejunum, ileum, cecum, and rectum, respectively.

Figure 5

Graphs of linear discriminant analysis effect size variance analysis of the abundances of bacterial taxa in different duck intestinal segments. (A–E) duodenum, jejunum, ileum, cecum, and rectum, respectively.

Figure 6

Functional analysis of the gut microbiota in ducks. (A) Tax4Fun functional distribution stack. (B) Microbial phenotypic abundance stack. (C) Welch's t-test,.

Figure 7

Analysis of cecal microbial diversity in ducks. (A) Host sequence filtering statistics. (B–F) ACE, Chao1, Shannon, Simpson, and PCA indices, respectively.

Figure 8

Gene prediction and functional annotation. (A) The distribution of the number of genes in each sample. (B) The distribution of the number of genes in subgroup violin plots. (C) CAZy annotation statistics. (D) The number of genes annotated to KEGG pathways. (E) Analyzing gene function differences with lefse.

Figure 9

Analysis of differential bacterial taxa in the cecum of ducks. (A–C) Stacked maps of cecal species distribution at the phylum, genus, and species levels, respectively. (D) Analyzing species differences with lefse. (E) Correlation analysis of relative abundance of cecal flora with growth performance at high and low residual feed intake.