Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels

Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg(−1) (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson’s correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-018-9533-0) contains supplementary material, which is available to authorized users.