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Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness - PubMed

  • ️Fri Jan 01 2016

Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness

Hui Yang et al. Sci Rep. 2016.

Abstract

Uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. Here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16S rRNA gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. Clostridium and SMB53 were enriched in the small intestine, while Prevotella, Treponema, Ruminococcus and Faecalibacterium showed a higher abundance in the cecum. Functional capacity analysis of gut microbiome revealed that the microbiome of small intestine plays important roles in the metabolism of small molecule nutrients, while the microbiome of cecum has the stronger ability to degrade xylan, pectin and cellulose. We identified tens of fatness associated-bacterial species including Escherichia spp. that showed a notable increase of relative abundance in all three gut locations of high fatness pigs. We further suggested that the potential pathogens, inflammation process, and microbial metabolism and nutrient sensing are involved in the high fatness of pigs. These results improve our knowledge about microbiota compositions in different gut locations, and give an insight into the effect of gut microbiota on porcine fatness.

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Figures

Figure 1
Figure 1. Alpha- and beta-diversity comparison of the microbiomes of the jejunum, ileum and cecum.

Analyses were performed on 16S rRNA V4 region data. Sample names are coded by breed (Lw, Laiwu breed), sampling site (Je, Jejunum; Il, Ileum; Ce, Cecum) and fat deposition status (Ob, high fatness; Le, low fatness). For example, LwIlOb represented the sample that was collected from the ileum of Laiwu pig with high fatness. The samples with the same Arabic numeral in the sample name were harvested from the same pig. (A) Alpha-diversity comparison based on shannon’s diversity index, grouped by sampling site and fat deposition status (mean ± SEM). Compared to the ileum and jejunum, the cecum has the significantly higher microbial richness. (B) Unweighted UniFrac principal coordinate analysis by bacterial microbiota. The small intestine (ileum and jejunum) and cecum samples show clear separation (C) Bray-curtis cluster tree. The samples from the same gut location trend to cluster together.

Figure 2
Figure 2. Taxonomic profiles of the microbial communities of the jejunum, ileum and cecum derived from 16S rRNA gene sequencing data.

(A) Microbial composition at the phylum level. Samples are represented along the horizontal axis, and relative abundance is denoted by the vertical axis. (B) Heatmap showing the 18 genera with significant differences of relative abundances among three gut locations. Heatmap is color-coded based on row z-scores.

Figure 3
Figure 3. Heatmap of gut luminal samples for bacterial species, CAZy function terms and KEGG subsystems from metagenomic sequencing data.

(A) Heatmap depicts the relative abundances of the 21 bacterial species significantly enriched in jejunum, ileum and cecum. (B) Heatmap of CAZy functional terms that showed significantly different enrichments among jejunum, ileum and cecum. GH: Glycoside Hydrolase, GT: GlycosylTransferase, PL: Polysaccharide Lyase, CE: carbohydrate esterases, CBM: Carbohydrate-Binding Module. (C) Heatmap of KEGG subsystems significantly enriched in jejunum, ileum and cecum.

Figure 4
Figure 4. Comparison of functional capacities of the gut microbiomes between high and low fatness pigs.

(A–C) show the comparisons of the relative abundances of CAZy functional terms between high and low fatness pigs in jejunum, ileum and cecum, respectively. GH: Glycoside Hydrolase, GT: GlycosylTransferase, PL: Polysaccharide Lyase, CE: carbohydrate esterases, CBM: Carbohydrate-Binding Module. (D–F) indicate the comparisons of the relative abundances of KEGG subsystems between high and low fatness pigs in jejunum, ileum and cecum.

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