Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb

Abstract

The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples. Our data suggest that a 30-day lamb has already developed mature microbial functions in the forestomachs, while the effect of the milky diet appears to be more evident in the remaining GITs. We also report the distribution and the relative abundance of the host functions, active at the GIT level, with a special focus on those involved in digestive processes. In conclusion, this pilot study supports the suitability of a metaproteogenomic approach to the characterization of microbial and host functions of the lamb GITs, opening the way to further studies aimed at investigating the impact of early dietary interventions on the GIT microbiota of small ruminants.

Keywords: metaproteomics; microbial community; mucosa; ruminant; sheep.

Figure 1

Alpha-diversity and richness distribution along the gastrointestinal tracts of a pre-weaned lamb. (A) Line graphs illustrating Shannon index values (alpha-diversity) computed based on taxonomic families (left), according to 16S data, and both host and microbial functional families (right), according to metaproteomics data, for each luminal and mucosal gastrointestinal sample. (B) Same as (A), but concerning richness (number of observed taxonomic families, left, and both host and microbial functional families, right).

Figure 2

Beta-diversity at taxonomic and functional level within the gastrointestinal tracts of a pre-weaned lamb. PCA plots were generated starting from the relative abundance of taxonomic families according to 16S data (A), microbial functional families (B), and host functional families (C), according to metaproteomic data. Each dot indicates a sample, while each color corresponds to a different gastrointestinal tract, with color-filled dots corresponding to luminal and empty dots to mucosal samples.

Figure 3

Top 10 most abundant taxonomic families along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial families identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to 16S data is reported. L, luminal; M, mucosal.

Figure 3

Top 10 most abundant taxonomic families along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial families identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to 16S data is reported. L, luminal; M, mucosal.

Figure 3

Top 10 most abundant taxonomic families along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial families identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to 16S data is reported. L, luminal; M, mucosal.

Figure 4

Top 10 most abundant microbial functions and metabolic pathways along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial functions (left) and metabolic pathways (right) identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to metaproteomic data is reported. L, luminal; M, mucosal; P, phosphate; DH, dehydrogenase; sub, subunit.

Figure 4

Top 10 most abundant microbial functions and metabolic pathways along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial functions (left) and metabolic pathways (right) identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to metaproteomic data is reported. L, luminal; M, mucosal; P, phosphate; DH, dehydrogenase; sub, subunit.

Figure 4

Top 10 most abundant microbial functions and metabolic pathways along the gastrointestinal tracts of a pre-weaned lamb. The relative abundance of microbial functions (left) and metabolic pathways (right) identified in the forestomach (A), small intestinal (B), and large intestinal (C) tracts according to metaproteomic data is reported. L, luminal; M, mucosal; P, phosphate; DH, dehydrogenase; sub, subunit.

Figure 5

Heatmap illustrating host digestive functions distribution along the gastrointestinal tracts of a pre-weaned lamb. Columns represent samples, while rows represent functions. Grey squares correspond to no-detected features. Only functions with mean relative abundance >0.001% are shown.