High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity

Abstract

Synbiotics are feed supplements with the potential to promote health and productivity in pigs partly, through modulation of the intestinal microbiome. Our study used shotgun sequencing and 16S rRNA gene sequencing techniques to characterize the effect of a synbiotic containing three Lactobacillus species and a fructo-oligosaccharide on the proximal colonic microbiome of 4- to 7-month-old Korean native black gilts. With shotgun sequencing we constructed unique metagenome-assembled genomes of gut microbiota in Native Black Pig for the first time, which we then used for downstream analysis. Results showed that synbiotic treatment did not alter microbial diversity and evenness within the proximal colons, but altered composition of some members of the Lactobacillaceae, Enterococcaceae and Streptococcaceae families. Functional analysis of the shotgun sequence data revealed 8 clusters of orthologous groups (COGs) that were differentially represented in the proximal colonic microbiomes of synbiotic-treated Jeju black pigs relative to controls. In conclusion, our results show that administering this synbiotic causes changes in the functional capacity of the proximal colonic microbiome of the Korean native black pig. This study improves our understanding of the potential impact of synbiotics on the colonic microbiome of Korean native black pigs.

Figure 1

Microbiome profiling results from 16S rRNA gene amplicon sequencing. (A) Alpha diversity of the microbial communities within samples in the study groups. (B) Principal coordinate analysis (PCoA) plot of the beta diversity based on the Bray–Curtis dissimilarity index between microbial community samples in the study groups. (C) Relative composition of the two dominant phyla based on taxonomic analysis of the 16S rRNA amplicon sequence data.

Figure 2

Analysis of the Metagenome-Assembled Genomes (MAGs) obtained using a host-customized database. (A) Phylogenetic tree of MAGs (B) rate of classified reads using standard database and custom database in kraken2. (C) Volcano plot for differentially abundant taxonomies. Each point represents the species-level taxonomies colored with phylum taxa. The taxa are presented with log₂ fold change (X-axis) and log₁₀(FDR-corrected P-value) (Y-axis). Horizontal line represents P-value cut off (FDR P-value 0.01). (D) Differentially abundant taxonomies (FDR < 0.01) between groups. Red bars represent composition in samples from the treatment group while gray bars, composition in samples from the control group.

Figure 3

Functional Profiling from shotgun metagenome sequencing. (A) Antibiotic resistance genes identified from each sample. (B) Bar chart for differentially abundant genes between groups. FDR P-value 0.0005 was used as threshold. (C) Taxonomic composition profiling at gene-level. (D) Clusters of Orthologous Groups (COG) functional category profiling results. (E) Bar chart for differentially abundant KEGG Ortholog functional category. Used FDR P-value was 0.05.