Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing

SIMPLE SUMMARY: Diarrhea in newborn piglets is one of the important problems for the agricultural industry. It is believed that this disease is associated with changes in the intestinal microbiome. The present work is aimed at studying the composition of the microbiome of newborn piglets with diarrhea in order to identify relevant markers of the disease. Our comprehensive microbiome study did not reveal bacterial and eukaryotic aberrations in the fecal microbiome of diarrheal piglets; at the same time, we observed higher levels of bacterial diversity, which may be associated with dysbacteriosis and inflammation. In the observation group, an increase in the abundance of Bacteroides B40-8 phage was also recorded, and in the healthy group, an increase in the abundance of Escherichia virus BP4. Thus, the results of our study show the ambiguity of the previously proposed relationship between the bacterial community of the fecal microbiome of suckling piglets and the development of diarrhea, and also indicate the need for further research in this area. ABSTRACT: Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.