Microbiota (16S rDNA sequencing) and microbiome (shotgun sequencing) data of a pig model of undernutrition.

The concept that gut microbiome-expressed functions are key regulators of ponderal growth has implications for child health and could provide new approaches for rearing farm animals that are key sources of high-quality protein in our food systems. We developed a feature-reduction algorithm to identify characteristics distinguishing the microbiomes of pigs that experienced diet restriction (DR) in utero and as they consumed a sequence of commonly administered postnatal diets, from the microbiomes of full-fed (FF) animals. The reduced growth of DR pigs is accompanied by reduced representation of microbial genes involved in degrading dominant components of their 'finisher-phase' diets, reduced levels of butyrate, a key host-accessible energy source produced by microbial fermentation of dietary polysaccharides, and significant increases in plasma triglycerides, glucogenic amino acids and urea cycle precursors and reductions in IGF-1. Gnotobiotic mice colonized with DR and FF fecal microbiomes and subjected to controlled feeding with the pig finisher diet revealed a causal relationship between the DR microbiome, reduced butyrate generation, and reduced liver fatty acid oxidation - effects that would contribute to impaired ponderal growth in pigs. The approaches described could help develop guidelines for stewardship of animal microbiomes in ways that support their healthy growth.