The impact of human-facilitated selection on the gut microbiota of domesticated mammals

Abstract

Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated–feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

“…A similar trend was observed for dogs and cats. Indeed, several studies reported a higher abundance of the Bifidobacterium taxa in puppies and kittens during the lactation and post‐weaning phases when compared to adult cats and dogs (Jia et al ., 2011; Guard et al ., 2017; Alessandri et al ., 2019a–c).…”

“…Beyond its metabolic role in providing nutritional support to the host by degrading otherwise non‐digestible dietary compounds coupled with the production of various SCFAs and other metabolites that provide nutrients to colonocytes, the gut microbiota is believed to be engaged in a continuous dialogue with the host’s immune system (Honneffer et al ., 2014). Notably, the intestinal microbial community modulates local and/or systemic immune responses, promotes intestinal barrier integrity, influences bowel homeostasis and functionality, and provides protection against enteropathogen colonization (Pickard et al ., 2017; Alessandri et al ., 2019a–c; Goto, 2019). The interactions between intestinal bacteria and the host immune system may be regulated either through direct contact between intestinal microorganisms and the innate immune system or indirectly by the release of microbial metabolites.…”

Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls, and Challenges

“…Besides, organisms used in tests are often sourced from rearing facilities, and have thus experienced domestication, a process documented to lead to massive changes in bacterial microbiome compositions. In vertebrates, changes include overall bacterial species richness decrease and shift in taxa abundances due to dietary, social, and environmental conditions of captivity [reviewed in (42,44)]. Effects in other taxa are less documented and less clear-cut.…”

Supplemental selenium source on gut health: insights on fecal microbiome and fermentation products of growing puppies

“…Among external factors, diet is the one that most rapidly alters the gut microbiome (Alessandri et al . 2019 ), having a positive or a negative impact on the host health and well-being.…”