Small intestinal morphology is one of the main criteria used for the evaluation of the intestinal physiology [
21]. Moreover, the morphometric assay, villus height, crypt depth, villus height/crypt depth (V/C) ratio, and villus surface area, are usually employed for the evaluation of the digestive and absorptive capacity of the intestine. Our results indicated that the FR housing did not have any effects on the intestinal histomorphological features of rabbits, showing overlapping aspects in both groups analyzed and suggesting that the outdoor rearing provides an adequate development of the enteric structural components. Similarly, no significant differences were found on the TABC and TMAC caecal content in the studied groups. Otherwise, microbial loads showed significant difference for the
E. coli count, with the lower content in the FR rabbits (2.45 and 3.01 log CFU/g in FR vs CS rabbits, respectively; p<0.05). The most common disorder in rabbit production is the occurrence of enteritis.
E. coli and
Clostridium spp. are two potential pathogenic bacteria frequently present in diarrheic rabbits and can lead to mortalities after weaning in excess of 20% [
22,
23]. Broadly, the term “gut health” describes the interaction between the intestinal wall barrier, the microbiota, and the immune components, which permit organisms to cope with internal and external stressors [
24,
25]. It is well known that the intestinal wall represents a natural barrier against pathogens and toxic substances present in the intestinal lumen. Also, the intestinal microbiota plays an important role in metabolic, nutritional, physiological and immunological processes [
26]. Previous research has shown that the housing environment may influence the gut microbiota structure in livestock species. Schreuder et al [
15] referred that in laying hens a cage-free system generated higher gut microbiota diversity compared to caged layers, and that the diet had a relatively lower effect on changing the gut microbiota, suggesting that the outdoor access and contact with soil and natural vegetation are likely important in raising gut microbiota diversity [
27]. As considered by Round and Mazmanian [
28] and Lee et al [
29], greater microbial gut variability translates into improved immune and metabolic performances. Our hypothesis was that the lower
E. coli caecal count found in rabbits reared under FR conditions could be related to an increase of gut microbiota diversity as well as to the improvement of gut health and well-being that enhanced the natural function of the intestinal barrier against pathogens.
In order to produce high-quality meat, it is necessary to understand the characteristics of meat quality traits and factors to control them [
30]. The housing system is one of the factors, which moderately affect rabbit carcass and meat quality [
31]. It should be enounced that meat comprises numerous tissues such as adipose, epithelial, connective and nervous tissues, even as the major component is muscle, thus the study of the muscles’ microscopic structures may provide useful information about the meat quality traits. Myofiber structure, diameter and organization, and collagen structure, thickness and distribution, have shown an important influence on the meat quality traits, indeed numerous studies have shown the relationship between meat quality attribute and fiber characteristic [
30]. Total number of fibers (TNF) and cross-sectional area of fibers (CSAF) are the primary morphology traits that influence the development of muscle mass as well as the meat quality [
29]. Also, contractile and metabolic assets of muscle are linked to fiber type composition (FTC) in muscle [
32,
33]. Moreover, the muscle fiber characteristics are significant for growth performance, for instance, Lee et al [
34] shown that the TNF and CSAF are significantly correlated with growth rate and carcass productivity of examined pigs. The meat sensory properties are also influenced by various structural properties of the muscle tissue like intramuscular fat (IMF) content and spatial organization, collagen content and spatial organization, myofibers spatial organization, type, size, shape and density [
35]. In particular, the meat fibers and the spatial organization of the conjunctive network of fat, which defines the “meat grain”, are one of the meat structure traits firmly related to meat tenderness. Moreover, meat texture and firmness are also influenced by the size of muscle fiber, the amount of connective tissue, and the quantity of subcutaneous and IMF [
30]. Among others, myofibrillar structure is highly influenced by the animal rearing conditions [
35]. Greenwood et al [
36] found that single- or multiple-reared lambs present significant differences in myofiber types, whereas Gondret et al [
18] reported changes in myofiber types according to indoor or outdoor rearing systems in rabbits. Recent knowledge underling the importance of assess the transition mechanisms that influence the FTC. Furthermore, it has now long been proven that physical activity positively affects this parameter [
30]. The more space available and the greater freedom of movement in outdoor housing conditions increased the physical activity of rabbits. According to Lefaucheur and Vigneron [
37], the FTC can be changed by physical exercise, depending on the type and duration of the activity. In addition, Ouhayoun [
38] referred that the increased movement affects muscle fiber type and size, which can increase the proportion of so-called “red” to “white” muscle fibers, which differ in their mitochondria or myoglobin content, and can affect the colour of the meat. Indeed, the exercise raises the oxidative capacity of the muscle, which increases the proportion of oxidative myofibers and the myoglobin content, thus influencing the meat redness [
18]. Accordingly, Krunt et al [
10] observed also increases in redness of the
Quadriceps femoris muscle in pen-housed rabbits. The increase in meat redness can be explained by the fact that as animal movement increases the number of mitochondria in αW fibers, converting their predominant glycolytic energy metabolism into oxidative energy metabolism and then, part of the αW fibers turn into αR fibers, richer in myoglobin [
39]. In contrast, reduced movements increase the muscle glycogen storage used for the anaerobic energy metabolism [
38]. The greater development of the hind part of the carcass of rabbits with more opportunities for physical activity has also been reported by other studies investigated housing systems which allow for different degrees of physical activity [
6,
40]. Gondret et al [
18] proved that subjecting rabbits to jumping exercises for 5 weeks significantly increased the development of the hind parts compared to rabbits that were not exercised. D’Agata et al [
1] referred that increasing physical exercise in FR housing raised the development of rabbit hind legs. It was theorized that the augment in physical activities could impacts the sizes of the muscles tissue, thereby affecting features such as yield, colour, and shear force [
10]. Thus, the alternative housing system, complying with the conditions of animal welfare, well fit the increasing consumers demand for home-made products and high-quality animal products [
2]. Our results showed that the FR system did not influence the muscle structure, and the histological assay of the spatial organization and the composition of muscle samples from FR rabbits satisfied the major parameters related with the meat quality traits.
Furthermore, as demonstrated by the low microbial counts, the sample of muscles tested in this study showed an optimal microbiological quality at slaughter, with lower TMAC in FR vs CS rabbits, and the absence of the
Enterobacteriaceae and
E. coli strains in all the samples analyzed. The initial microbial load of meat is influenced by the physiological status of the animal and by the hygienic state during slaughter, and production processes [
41]. Moreover, Pereira and Malfeito-Ferreira [
42] have highlighted the importance of a low microbial count on rabbit meat shelf-life, assuming that also growth parameters are influenced by the initial contamination [
43]. In addition, rabbit meat is more prone to lipid oxidation than other meats, and it can easily permit the growth of pathogenic and spoilage microorganisms [
42,
44]. Tufarelli et al [
11] found that muscles from FR rabbits showed an improvement in the oxidative stability in respect to the group reared in conventional cage. In particular, the meat from FR rabbits had a lower thiobarbituric acid-reactive substances level compared to CS rabbits, suggesting that the housing system may fortify the meat oxidative stability. It’s well known that environmental stress may influence the oxidative processes in the body, disrupting the balances between oxidative-antioxidative reactions and leading to an increase of production of reactive oxygen species that progress the detrimental oxidative changes in organic tissue. In turn, the meat oxidative stability influences the shelf life and the microbiological quality of the muscles. In the present study, the lower TMAC and the absence of
Enterobacteriaceae and
E. coli strains found in rabbits reared in FR system suggested that this rearing system allows an improvement of the hygienic conditions and rheological characteristics of meat that could be also related to a reduction of stress as well as an increase of rabbit well-being promoted by the alternative farming system.