Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF pigs

The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. Here, we focus on the comparison of gut microbial communities in miniature pigs developed for xenotransplantation in specific pathogen-free (SPF) and conventional (non-SPF) facilities. To identify the disparities in gut microbial composition and functionality between these two environments, 16S RNA metagenome sequencing was conducted using fecal samples. The results revealed that the non-SPF pigs had higher gut microbiota diversity than the SPF pigs. The genera Streptococcus and Ruminococcus were more abundant in SPF pigs than in non-SPF pigs. Blautia, Bacteroides, and Roseburia were exclusively observed in SPF pigs, whereas Prevotella was exclusively found in non-SPF pigs. Carbohydrate and nucleotide metabolism, as well as environmental information processing, were predicted to be enriched in SPF pigs. In addition, energy and lipid metabolism, along with processes related to genetic information, cellular communication, and diseases, were predicted to be enriched in non-SPF pigs. This study makes an important contribution to elucidating the impact of environments harboring a variety of microorganisms, including pathogens, on the gut microbiota of miniature pigs. Furthermore, we sought to provide foundational data on the characteristics of the gut microbiota in genetically modified pigs, which serve as source animals for xenotransplantation. Overall design: A total of 8 Massachusetts General Hospital (MGH) miniature pigs (4 SPF and 4 non-SPF pigs) from National Institute of Animal Science were enrolled into this study. The SPF facility employs high efficiency particulate air (HEPA) filters to introduce filtered air, preventing exposure to animals in the general environment and thereby mitigating the risk of pathogens that could infect pigs. In order to support SPF pig production and management, the facility conducts regular testing for 42 types of pathogens. SPF pigs were bred in sterilized isolator (the positive pressure of 5 mmH2O, humidity of 50%) and fed artificially sterilized milk. The temperature was maintained at 38ºC for the first week and then decreased by 3? every week until 5th week after birth. After weaning, they were raised in the SPF level breeding cage with sterilized pellet-type commercial feed and sterilized water. Non-SPF pigs were naturally fed by the sow until 5 weeks of age and then gradually weaned in conventional facility. The fecal samples were obtained from SPF and non-SPF pigs at the age of 18 months.