Statistical study of the diarrhea factor using the Shotgun Metagenomic Sequencing technique of intestinal microbiome samples of Iberian pigs from 0 days of life to 90 days of age

Abstract

Abstract Background: Due to the increasing tendency to decrease the use of antimicrobials in piglets to mitigate intestinal dysbiosis problems, new alternatives are being sought for the control and prevention of these important pathologies in animals. Among these alternatives is the study of the intestinal microbiota of pigs. It is crucial to rule out or ensure that diarrhea is an influential factor in the composition of the piglet microbiome. The Next Generation (Shotgun) Whole Genome Sequencing technology has not been used for this purpose so far in Iberian pigs. Methods: The study aims to demonstrate statistically that the diarrhea of the piglets does or does not provide significant differences in relation to the relative abundance of the different taxa between samples, their alpha diversity, their beta diversity and in relation to the beta dispersion of their beta diversity. Studies on the relative abundances of different taxa and comparative studies of abundance of different taxa are carried out. The study also aims to discover which are the species that generate the greatest differences or contrast between the different samples according to the intestinal dysbiosis of the piglets studied. Results: Statistical inference tests determined that the diarrhea-related compositions of the samples are different according to the Phylums, that the beta diversities of the samples are also different in relation to the diarrhea factor and the age factor, while the beta dispersions of these two factors, diarrhea and age, are not different. The alpha diversities of the samples were not different in relation to the diarrhea factor. It is determined that there are species in the Microbiota of pigs that have also been found in humans and non-human primates, thus highlighting the importance of the One Health concept between the two species. Conclusions: The diarrhea factor and age generate evident differences in the composition of the microbiome of pigs. This porcine microbiome is closely related to the human microbiome in relation to the species that generate the greatest differences between piglets suffering intestinal dysbiosis and healthy pigs.