• Dietary variables had the largest effect on microbiota composition • Rustic and conventional rearing conditions led to differential microbiota profiles • Rustic rearing favoured Treponema -enriched, more-diverse microbial profiles • Enterotypes were associated with husbandry conditions and faecal water content • Underexplored taxa contributed to in vitro fibre fermentation and SCFA production The gut microbiota is shaped profoundly by the diet, environment, and genetics of its host. Yet, previous studies have focused primarily on investigating factors individually in standardised facilities. In the present study, faecal samples and rearing metadata were collected from a highly-diverse cohort of 344 pigs, from farms to the wild, spanning eight countries and two continents. We hypothesised that varied lifestyles would induce a range of diverse microbiotas. Rustic rearing conditions were associated with increased α-diversity, alongside Treponema , while conventionally-reared pigs exhibited increased Lactobacillus . Equally, both rustic-associated bacteria and conventional feed were associated with increased short-chain fatty acids. Gas production kinetics from in vitro fermentation revealed the complex role of underexplored bacteria in fibre fermentation. The present study represents one of the most diverse single-study cohorts of pigs hitherto, and underscores the complex interplay between swine husbandry and the gut microbiota, and in turn, its potential consequences for functionality.
Comer et al. (Sun,) studied this question.