Early-life feeding in piglets: the impact on intestinal microbiota and mucosal development

Choudhury, Raka


Early-life bacterial colonisation can be of particular importance to the overall growth and health of an animal, especially influencing intestinal and immune system development with long-term implications. This is especially relevant in pig production where post-weaning enteric infection is one of the major concerns related to the gut health of pigs, and is associated with economic losses and welfare problems. Commercial pig production systems involves early and abrupt weaning, which contrasts with the gradual transition from mother’s milk to solid feed in nature. Due to such abrupt weaning, a piglet is challenged with multiple stressors (including environmental-, nutritional- and psychological-) which is usually associated with changes in gut microbiota and a high incidence of diarrhoea. Modulating intestinal microbiota to reduce weaning-associated problems in pigs, is getting increasing scientific and commercial interest, as microbial dysbiosis (or imbalance) has been identified as a leading cause of post-weaning intestinal infections. The overall aim of this thesis was to understand the molecular effects of early-life feeding (pre-weaning provision of fibrous feed), associated with the pattern of intestinal microbiota colonisation and gut maturation. We hypothesised that early feeding of a fibrous diet containing both soluble and insoluble fermentable fibres will affect the microbiota and physiological development of neonatal or suckling piglets, facilitating a better preparation for the weaning transition.

First, we focussed on assessing an optimal sampling method to study microbiota development in neonatal piglets. We showed that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early-life, when faecal sampling is challenging. Although rectal swab samples bring a certain degree of variability with the presence of mucosa-adhered population, they also provide the opportunity to assess the impact of an intervention on the mucosa-adhered populations. The second aim of this thesis was to investigate the age-related gut microbiota colonisation and the impact of fibrous feed on the gut microbiota colonisation as well as intestinal physiology in neonatal piglets. We performed a longitudinal study (using rectal swabs) to evaluate the impact of early feeding (fibrous feed) on the microbiota colonisation at pre- and post-weaning time-points. The results revealed that the early-fed (EF) piglets had an accelerated maturation of the microbiota, compared to the control (CON) piglets that consumed milk exclusively. Accelerated maturation at pre-weaning time-points were characterised by the simultaneous emergence of typical post-weaning-associated microbial groups (such as Prevotella, Roseburia, Faecalibacterium, Ruminococcus, Megasphaera, Subdoligranulum) and a more rapid decline of typical early-life/pre-weaning microbial genera (e.g., Fusobacterium, Finegoldia, Bacteroides, Eschechichia-Shigella). Moreover, we found a quantitative association between eating behaviour of EF piglets (video scores) and their microbiota signature, indicating that the piglets who spent more time at the feeding trough had a higher abundance of ‘accelerated’ microbial groups. Furthermore, early feeding altered the colonic microbiota composition, increased microbial fermentation products (SCFA) in the colon and modulated intestinal development i.e., increased weights and lengths of several intestinal tract segments, as well as a decreased villus-crypt ratio in jejunal mucosa and an increased abundance of proliferative cells in colon mucosa, just before weaning. The third aim of this thesis was to evaluate the host mucosa transcriptome response due to pre-weaning fibrous feed. Maximum impact of early feeding was detected at weaning (day29; compared to other time-points), which was followed by convergence of the transcriptome three weeks post-weaning (day+21) in EF and CON piglets. We showed that early feeding not only accelerates the gut microbiota, but also the host transcriptome maturation at weaning. The results revealed that in the EF group, oxidative phosphorylation, cholesterol biosynthesis and oxidative stress-related pathways were significantly enriched, whereas sirtuin signalling and immune response pathways were downregulated in the colon mucosa at day29. Remarkably, three days after weaning, the EF piglets displayed a stronger mucosal responsiveness compared to the CON piglets, reflected in the increased expression of genes (transcriptomics) related to immune activation, epithelial migration and “wound-repair" like processes necessary to maintain gut barrier integrity (during weaning transition) as well as jejunal morphometry. In the last chapter, we explored fundamental aspects of host-microbe interactions, by evaluating the associations between the intestinal microbiota and behaviour of suckling piglets. We aimed to tentatively reveal associations between the intestinal microbiota composition and piglet behaviour in a test for coping style, (i.e. a personality trait), as well as anxiety- and exploration-related behaviour in a novel environment test. A number of microbial groups such as Coprococcus, CAG-873, Atopobium and Prevotella were identified to be associated with anxiety- and/or exploration-related behaviour, although these results are premature and need further validation for their biological relevance. Overall, the findings of this thesis indicate that EF piglets show an “alerted system” with an enhanced responsiveness to external stimuli of feed and microbiome development, compared to the CON group, thus exemplifying the potential of early-life programming to modulate intestinal development in piglets. Furthermore, the results of this thesis indicate that early feeding of fibrous feed has considerable potential to better prepare young piglets for the weaning transition.