Unraveling piglet gut microbiota dynamics in response to feed additives

Keywords: GI tract, microbiota, pig, PITChip, weaning

The gastrointestinal (GI) tract of pigs is colonized by a dense and metabolically active microbiota, comprising mainly bacteria, that have not only a commensal but a symbiotic (beneficial for both) relationship with the host. These bacteria are important for host health, as they provide the pig with essential products, form a key barrier against pathogens and are involved in development and homeostasis of morphology, digestion, and host immunity. The fact that the GI tract microbiota plays such an important role in pig health, allows to influence host health by modifying microbiota composition and activity. Supplementing pigs with diet ingredients that can have an effect on the GI tract microbiota is a common strategy to affect pig’s health, especially around the time of weaning. During weaning, piglets suffer a dramatic imbalance in composition and activity of the GI tract microbial community that, during the last decades, has been treated with antibiotics to control harmful micro-organisms. This practice has raised concerns in the last years due to the cross-resistance of pathogens to antibiotics used in humans, causing a ban on their use in the European Union from January 2006 onwards. This triggered an increased interest in finding alternatives for in-feed antibiotics, such as prebiotics, probiotics, organic acids and other plant-derived bioactive compounds. This thesis presents the results of various in vitro and in vivo studies addressing the response of piglet GI tract microbiota to the supplementation with different feed additives. To this end, we developed the Pig Gastrointestinal Tract Chip (PITChip), a semi-quantitative and high throughput diagnostic tool that allows us to gain novel insight in composition and dynamics of porcine GI tract microbiota at high taxonomic and spatiotemporal resolution. Furthermore, a specific and sensitive real-time PCR assay was developed for quantification of the pathogen Streptococcus suis. This revealed that abundance of S. suis in the piglet intestine increased after weaning, whereas that of Lactobacillus populations decreased. The application of the PITChip, together with other molecular tools, allowed us to follow microbial changes in time and in response to a range of different dietary supplements. Addition of sodium butyrate (SB) and different blends of organic acids had a significant effect on the microbial profiles in different sections of the GI tract, reinforcing previous reports on the antimicrobial effect of organic acids on piglet GI tract microbiota. SB administration most strongly affected populations within the Clostridium cluster XIVa and the Bacteroidetes. Results from different studies proved as well the antimicrobial effect of essential oils, and more specifically oregano oil (carvacrol), both in vivo and in vitro. The essential oil lowered overall microbiota diversity and relative abundance of members of Clostridium clusters IV and XIVa, and several Streptococcus- and Bacteroides-like species. In conclusion, the development and application of complementary molecular tools described in this thesis provided important information towards sound design of sustainable dietary strategies aiming at the replacement of in-feed antibiotics.