The fecal microbiota of piglets is influenced by the farming environment and is associated with piglet robustness at weaning

This study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal samples and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera were Prevotella, Faecalibacterium, Roseburia, and Lachnospira. They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding individual characteristics, piglets whose growth was less perturbed by weaning had more Bacteroidetes (P < 0.01) and less Proteobacteria (P < 0.001). In response to weaning, they showed a greater increase in Prevotella (P < 0.01), Coprococcus (P< 0.01) and Lachnospira (P < 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.