swine gut microflora Raw sequence reads. pig gut metagenome

The mammalian gut is a complex ecological niche, the microscopic inhibitors, gut microbiota (GM), are believed to be important for the health and development of animals: aiding colonic fermentation, stimulating the immune system, defensing pathogens, and improving energy harvest. In pigs, mass of studies were reported the GM of healthy pigs under different stages or breed. They demonstrated variance of GM alternations, as age grows, and weaning and colitis. In this study, we applied molecular techniques to investigate the GM in PEDV infected sows and controls, and the offsprings delivered by these sows. A 'mock' community (MC) was constructed by 15 evaluated bacterial species belong to 13 genera was set to evaluate the methods in this project. Thirty-four newborn piglets under different healthy states (healthy piglet, abbreviated as HP, N=4; asymptomatic piglet, AP, N=15; diarrheal piglet, DP, N=15) were sampled, together with their respective mothers (health sow, HS, N=3; asymptomatic sow, AS, N=4; diarrheal sow, DS, N=4). Faecal microbiota were assessed by 16S rRNA gene pyrosequencing on V1-V3 hypervariable regions. Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present sows under different healthy status. For piglets, dive dominated phyla, Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Actinobacteria, encompass more than 99% in abundance in overall subjects. The abundances of inflammatary or diarrhea associated bacteria from Desulfovibrionaceae, Desulfovibrio, and Clostridium perfringens, Clostridium difficile were significantly increased (p<0.05) while the butyrate-producing bacterium, Clostridium butyricum etc., were reduced in diarrheal sows when compared those with the healthy sows. For piglets within 10-day-old, the abundances of short-chain fatty acid producing bacteria of Prevotella, Bacteroides, Coprococcus and Bacteroides, and the butyrate-producing bacterium Clostridium butyricum were remarkably decreased in diarrheal and asymptomatic piglets when compared those to the healthy piglets.