Microbiota digestiva del cerdodeterminación del patrón en condiciones de salud y enfermedad

Zusammenfassung

Gut microbiota has a great impact on animal health participating in several physiological functions. In recent years, non-specific digestive diseases associated with dysbiosis or microbial imbalance of this microbiota have gained significant relevance in swine. Moreover, the control of the most common swine digestive infections is mainly based on the use of antimicrobials, although the legislation is increasingly restrictive regarding its use for prophylactic or metaphylactic purposes. For this reason, there is an urgent need to develop new therapeutic approaches such as changes in the diet or supplementing it with organic acids, plant extracts or probiotics and prebiotics which modify, restore or correct imbalances of this gut microbiota. However, before the implementation of these new control strategies, it will be necessary to expand our knowledge on the swine gut microbiota and to develop tools that will allow the evaluation of its composition in field conditions in a systematic and efficient way. This study focuses on the characterization of gut microbiota in swine during the first weeks of life in both healthy and diseased animals suffering from digestive disorders associated with dysbiosis as well as the animals receiving different diets. The final aim is to advance in the development and evaluation of new interventions for the control of enteric disorders avoiding the use of antimicrobials in swine production. Quantitative PCR or qPCR was the chosen technique for the study of the composition and evolution of gut microbiota, a faster and more economical method than the massive sequencing of the microbiota DNA. Populations of total bacteria, bacteroides, lactobacilli, enterobacteria, bifidobacteria and Clostridium clusters I, IV and XIV were quantified in twelve experimental studies which included lactation, weaning, nursing and the first half of the fattening period. An ELISA for the quantification of lactoferrin, a biomarker of intestinal inflammation, was also developed and optimized in piglet faeces. The comparison of the results given by the qPCR assays and those of the massive sequencing based on the amplification of the 16S rRNA, gold-standard for the study of gut microbiota, showed a high correlation between the estimates obtained using both techniques. Monitoring of gut microbiota from birth to the fattening period showed a progressive increase in bacteroides and a decrease in lactobacilli and enterobacteria, although this latter population was slightly higher at weaning. Populations of bifidobacteria and the three Clostridium clusters remained relatively stable throughout the follow-up period, although Clostridium clusters IV and XIV showed a lower concentration during the first few days of life. The comparison between healthy and diseased piglets with clinical signs compatible with dysbiosis detected several significant differences. Gut microbiota of the healthy piglets showed lower numbers of enterobacteria and higher concentrations of lactobacilli and Clostridium clusters IV and XIV. However, lactoferrin concentration in faeces was similar in both groups of animals, with no evidence of intestinal inflammation. There were also limited differences in the composition of gut microbiota in piglets sharing genetics and diet but reared on farms with different healthy standards. Piglets from farms with a high health standard presented a better microbiota composition at birth while piglets from low standard farms showed, throughout the follow-up, a lower diversity in their microbiota, a fact that has been associated with a greater susceptibility to infections. Finally, different diet interventions were evaluated. The supplementation with zinc oxide reduced enterobacteria population in the faeces of weaned piglets and thus decreasing the risk of post-weaning diarrhoea. The reduction of antibiotics in the diet had a limited effect on the bacterial composition of gut microbiota, with lower numbers of bacteroides. The addition of medium chain fatty acids was associated with a significant increase of bacteroides and Clostridium clusters IV and XIV, microorganisms which produce short chain fatty acids, while the increase of fiber in the diet through the supplementation with oatmeal did not increase the richness of the microbiota, the opposite to that previously proposed, and was associated with a reduction in the population of Clostridium cluster IV in one of our experimental studies.