Simple SummaryThe use of low-cost by-products originating from agri- and dairy-chain production in animal nutrition represents an alternative strategy to feed and improve animal performance and reduce the environmental impact. In swine production, liquid-feeding products can positively contribute to the equilibrium of animal guts, thus supporting the reduction of feed medication. The liquid whey by-product of the cheese-making process is considered a palatable alternative feed and a promptly available source to provide functional ingredients without further costly transformation. In the last decade, increased knowledge of the gut microbiome has contributed to expanding our insights on host health, well-being, growth, and feed efficiency. Based on this perspective, this research investigated the fecal microbiota of crossbred pigs that underwent a co-feed liquid whey-integrated diet with a metagenomics approach.AbstractThis study assessed the potential effect of a co-feed liquid whey-integrated diet on the fecal microbiota of 14 crossbred pigs. The experimental design was as follows: seven pigs were in the control group, fed with a control feed, and seven were in the experimental group, fed with the same control feed supplemented daily with liquid whey. The collection of fecal samples was conducted on each animal before the dietary treatment (T0) and one (T1), and two (T2) months after the beginning of the co-feed integration. In addition, blood samples were collected from each pig at the same time points in order to evaluate the physiological parameters. Taxonomic analysis showed a bacterial community dominated byFirmicutes,Bacteroidetes,Spirochaetes, andProteobacteriaphyla that populated the crossbred pig feces. The diversity metrics suggested that the co-feed supplementation affected some alpha diversity indexes of the fecal microbiota. In addition, the differential abundance analysis at the genus level revealed significant differences for various genera, suggesting that the liquid whey supplementation potentially influenced a part of the bacterial community over time. Spearman’s correlations revealed that the differential abundant genera identified are positively or negatively correlated with the physiological parameters.