Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

Abstract

The present study aimed at investigating the evolution of pigs’ fecal microbiota composition from post-weaning to finishing in a longitudinal analysis. The experiment was conducted on 160 Pietrain × (Large White × Landrace) castrated male and female pigs in two replicates. Feces were collected at 52, 99, 119, 140, and 154 days of age for further 16S rRNA sequencing to analyze the microbiota composition. Pig microbiota evolved strongly from 52 to 99 days of age with an increased abundance of Streptococcaceae and a decreased abundance of Lactobacillaceae. During the finishing stage, microbiota kept evolving at a slower rate. To link the community structure to the performances, the fecal samples were clustered into enterotypes sharing a similar bacterial composition. At 52 days, two enterotypes dominated either by Lactobacillus or by Prevotella–Sarcina were identified. They differed from the two enterotypes determined from 99 to 154 days which were dominated either by Lactobacillus or by Turicibacter–Clostridium sensu stricto. During this time period, 75% of the pigs switched enterotypes. The enterotypes were not related to differences in the overall growth or feeding performance. The enterotype definition was time-dependent and seemed to be related to the sex type at 99 days of age.

Learning machine approach reveals microbial signatures of diet and sex in dog

“…For humans, geographical or ethnic variations, host genetic, immunity, lifestyle and diet or dietary habits have been reported as factors affecting gut microbiota [21]. Sex [22], genetic performances [23], phase of growth, other than diet [24] have been reported to influence gut microbiota in pigs. In healthy dogs, variations of microbiome with age, from weaning to adulthood, were reported [25,26], with a stabilization of the core gut microbiota at maturity.…”

Changes of Gut Microbiota and Its Correlation With Short Chain Fatty Acids and Bioamine in Piglets at the Early Growth Stage

“…Accumulating information about the gastrointestinal tract microorganisms of pigs has been obtained since the extensive application of "omics analysis" (3)(4)(5)(6)(7). It is believed that the gut of neonates is devoid of microbes prior to birth but rapidly undergoes a marked shift from an essentially germ-free state to harboring an extremely dense microbial population that eventually experiences microbial succession and establishes an adult-like microbial community (7)(8)(9).…”

Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

“…However, gut microbiota varies largely among individuals on time and space scale [ 17 ], which is an obstacle to a better understanding of the complex biological effects of the microbiome. Population stratification is a useful approach to cope with the obstacle, which has found that several equilibrium states—i.e., enterotypes (ETs)—are possible [ 18 ]. The term “enterotype” was first raised by Arumugam et al in 2011, referring to distinct community composition types of human gut microbiota [ 19 ].…”

“…Ramayo-Caldas et al found that the ET-like clustering was significantly associated with the pig feed efficiency and growth traits, suggesting the ET concept may have an important role in the pig production industry [ 26 , 28 ]. Although relatively robust, ETs are demonstrated to be strongly associated with the pig age, long-term diets, and even different clustering and grouping strategies [ 18 , 28 , 29 , 30 , 31 ]. However, knowledge is also limited to the effects of the different ETs on the butyrate metabolism in pigs.…”