Fecal microbiota-based investigations of nitrogen utilization efficiency and related traits in a Landrace × Piétrain crossbred population.

Improving protein efficiency in pork production is a desired goal regarding resource conservation and climate protection, whereby animal breeding has great potential for sustainable improvements. Nitrogen utilization efficiency (NUE) is an important trait but laborious to measure. As blood urea nitrogen (BUN) can be used to predict NUE, it is often used as indicator trait. Both NUE and BUN were found to be heritable; however, microbial studies have not yet been carried out. The present study aimed to investigate the role of the gastrointestinal microbiota in the context of N efficiency in different fattening phases. The dataset consisted of 450 Landrace × Piétrain pigs fattened in a 2-phase feeding regime. All pigs were fecal sampled and phenotyped in 2 fattening phases, referred to as sampling period (SP) 1 and SP2, in week 13 and week 16 post natum, respectively. Microbial communities in feces were compared across SPs, and significant differences were observed. Mixed linear models were applied to quantify the microbial variance and microbiability for NUE, BUN, and related traits within each of the SPs. Except for NUE in SP1, all microbiabilities were significant and ranged from 0.079 to 0.471. Microbiome-wide association studies revealed a polymicrobial trait architecture characterized by the contribution of many genera, with each genus having a relatively small effect on the traits. In total, 4 and 11 microbial genera were significantly associated with NUE and BUN, respectively. Microbial correlations were estimated between traits within SPs via bivariate analyses. Blood urea nitrogen was significantly correlated with N intake and retention in SP1 but not in SP2. Fecal microbiota composition differed significantly between SPs and the use of microbiota data across SPs resulted in a remarkable drop in microbiability for nearly all traits. This implies that microbiota data should be representative of the time point of phenotyping to fully capture microbial contribution to trait expression. The results suggest that jointly using genomic and fecal microbial data might be expedient to improve protein efficiency in fattening pigs.