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Background  The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularly between selection nucleus and commercial populations. In this paper, we investigated fecal microbial composition in nucleus versus commercial systems at different time points.    Results  We identified microbial OTUs associated with growth and carcass composition in each of the two populations, as well as the subset common to both. The two systems were represented by individuals with sizeable microbial diversity at weaning. At later times microbial composition varied between commercial and nucleus, with species of the genus  Lactobacillus  more prominent in the nucleus population. In the commercial populations, OTUs of the genera  Lactobacillus  and  Peptococcus  were associated with an increase in both growth rate and fatness. In the nucleus population, members of the genus  Succinivibrio  were negatively correlated with all growth and carcass traits, while OTUs of the genus  Roseburia  had a positive association with growth parameters.  Lactobacillus  and  Peptococcus  OTUs showed consistent effects for fat deposition and daily gain in both nucleus and commercial populations. Similarly, OTUs of the  Blautia  genus were positively associated with daily gain and fat deposition. In contrast, an increase in the abundance of the  Bacteroides  genus was negatively associated with growth performance parameters.    Conclusions  The current study provides a first characterization of microbial communities' value throughout the pork production systems. It also provides information for incorporating microbial composition into the selection process in the quest for affordable and sustainable protein production in swine.    Supplementary Information  The online version contains supplementary material available at 10.1186/s42523-021-00118-z.

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs