The adaptability of livestock to changing environments is based in particular on their genetic characteristics but also on the farming conditions to which they are subjected. However, this last point is poorly documented and little is known about its contribution to environmental challenges. The study by Quéméner and colleagues [1] addresses this question by assessing the effect of two hygiene conditions (good vs poor) on the distribution of cell populations present in adipose and muscle tissues of pigs divergently selected for feed efficiency [2]. The working hypothesis is that degraded housing conditions would be at the origin of an hyper stimulation of the immune system that can influence the homeostasis of adipose tissue and skeletal muscle and consequently modulate the cellular content of these tissues. Cellular compositions are thus interesting intermediate phenotypes for quantifying complex traits. The study uses pigs divergently selected for residual feed intake (RFI+ and RFI-) to assess whether there is a genetic effect associated with the observed phenotypes. The study characterized different stromal cell populations based on the expression of surface markers: CD45 to separate hematopoietic lineages and markers associated with the stem properties of mesenchymal cells: CD56, CD34, CD38 and CD140a. The authors observed that certain subpopulations are differentially enriched according to the hygiene condition (good vs poor) in adipose and skeletal tissue (CD45-CD56-) sometimes with an associated (genetic) lineage effect. This pioneering study validates a number of tools for characterizing cell subpopulations present in porcine adipose and muscle tissue. It confirms that housing conditions can have an effect on intermediate phenotypes such as intra-tissue cell populations. This pioneering work will pave the way to better understand the effects of livestock systems on tissue biology and animal phenotypes and to characterize the nature and function of progenitor cells present in muscle and adipose tissue.