Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex

Dietary fiber content and composition affect microbial composition and activity in the gut, which in turn influence energetic contribution of fermentation products to the metabolic energy supply in pigs. This may affect feed efficiency (FE) in pigs. The present study investigated the relationship between the fecal microbial composition and FE in individual growing-finishing pigs. In addition, the effects of diet composition and sex on the fecal microbiome were studied. Fecal samples were collected of 154 grower-finisher pigs (three-way crossbreeds) the day before slaughter. Animals were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Fecal microbiome was characterized by 16S ribosomal DNA sequencing, clustered by operational taxonomic unit (OTU), and results were subjected to a discriminant approach combined with principal component analysis to discriminate diets, sexes and FE extreme groups (10 high and 10 low FE animals for each diet by sex-combination). Pigs on different diets and males vs. females had a very distinct fecal microbiome, needing only two OTUs for diet (P=0.020) and 18 OTUs for sex (P=0.040) to separate the groups. The two most important OTUs for diet, and the most important OTU for sex, were taxonomically classified as the same bacterium. In pigs fed the CS diet there was no association between FE and the fecal microbiota composition (P>0.05), but in pigs fed the WB diet differences in FE were related to 17 OTUs in male animals (P=0.018) and to 7 OTUs in female animals (P=0.010), with three OTUs in common for both sexes. In conclusion, our results showed a diet and sex dependent relationship between the fecal microbial composition at slaughter weight and FE in grower-finisher pigs.