Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract

Abstract

Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions.

Keywords: metaproteomics; microbiome; pig.

Figure 1

Relative distribution of proteins in digesta and mucosa samples of the pig into parasite, bacteria, pig, and uncharacterized proteins across gastrointestinal tract sections and compartments in four animals. Numbers 3, 7, 8, and 15 are pig identifiers.

Figure 2

Sample ordination to discriminate the protein distribution between mucosa and digesta samples (A), within the mucosa (B) and the digesta (C) samples. Principal Coordinate Analysis (PCoA) plots were drawn from protein data using S17 Bray Curtis similarity. The percentage represents the contribution of the principal component to the difference in sample composition. Points of different colors and shapes represent samples of different groups, and the closer the two sample points are, the more similar the composition of the samples species is.

Figure 3

(A) Averaged distribution of bacterial phyla in mucosa and digesta of the swine intestine. (B) Bacterial families (>1%) found in digesta and (C) mucosa of all animals in relative abundance (%) based on the number of peptides. Numbers of referring peptides are given beneath each bar. The fifth bar represents an average (Ø) of the section amongst all animals.

Figure 4

Distribution of proteins involved in single short chain fatty acid (SCFA) biosynthesis (A) and measured concentrations of single SCFA (B) in digesta samples shown for each section and pig. Color code is equal for A and B: light grey: formate, blue: acetate, dark orange: propionate, light orange: butyrate, grey: valerate. Proteins were sorted according to Polansky et al. [43] (Table S4).

Figure 5

Proteomaps of animal mucosa (left) and digesta (right) proteins per animal and section. Numbers 3, 7, 8, and 15 are pig identifiers. Abbreviations of protein groups are explained in Section 3.5.