The objective of the study was to investigate the effect of different protein sources and nutrient specification levels on the gut microbiome composition of nursery pigs.

A total of 120 crossbred gilts (Large White ´ Landrace ´ Duroc, initial BW 6.74 ± 0.06 kg, 18 days of age) were allotted to 1 of 6 treatments: animal protein source with nursery diet specifications (AN); animal protein source with grower diet specifications (AG); plant protein source with nursery specifications (PN); plant protein source with grower diet specifications (PG); plant protein source, nursery diet specifications, and an enzyme + essential oil cocktail (PN+EOE), and plant protein source, grower diet specifications, and an enzyme + essential oil cocktail (PG+EOE). There were 4 pigs per replicate and 5 replications per treatment, in a randomized block design. On d 43, 1 pig per replicate was sacrificed, and cecum and colon digesta samples were collected for gut microbiome analysis and profiled though MiSeq 16S rRNA sequencing. Data were analyzed using univariate and multivariate methods within R. No differences in alpha or beta diversity were detected based on protein source, nursery diet specification, or inclusion of EOE; however, a number of discriminating taxa were present between pigs fed treatments with different protein sources. For instance, abundance of Parabacteroides was increased in colonic PG samples (P = 0.01) compared with AG, and abundance of Lachnospiraceae was increased in all samples of AG compared with PG (P = 0.009). Eubacterium (P = 0.044) and Turicibacter (P = 0.031) were both more abundant in colonic AN samples when compared with PN samples.