Gut Microbiota Characteristics Of Piglets With Viral Diarrhea Based On High-throughput Sequencing Technology

The production and consumption of pigs in China has accounted for half of the total quantity in the world.The swine industry's output value exceeds 1.5 trillion yuan,which is an important industry affecting the national economy and people's livelihood.Pork,like grain,is the basic industry to ensure the food safety in China.However,there are still some factors restricting the sustainable and healthy development of swine industry.Piglet diarrhea,especially caused by virus,decreases the immunity of piglets and increases the mortality of piglets.Meanwhile,infection with viral diarrhea also leads to a decline in the slaughter rate of live pigs.Contaminated pork is the source of human disease,resulting in serious food safety and public health problems.In our study,samples were collected from a commercial swine farm located in Guangdong province.There were two suspected viral diarrhea outbreaks in April and July,2017.Fecal or small intestinal content samples were collected from piglets for viral detection and further study.The characteristics of gut microbiota of healthy piglets and piglets with viral diarrhea at specific age were detected by Illumina MiSeq high-throughput sequencing technology.1.Fresh fecal samples were collected from 1�3-week-old healthy piglets(n = 20)and PEDV infected piglets(n = 20)from a commercial swine farm located in Guangdong province in April 2017.Intestinal contents samples were collected from 7-days healthy piglets(n = 3)and diarrhea piglets(n = 10)from the same swine farm in July 2017.Colloidal gold kit and RT-PCR were used to detect the possible infected virus.The results showed that the healthy piglets were negative for porcine epidemic diarrhea virus(PEDV),porcine rotavirus(PoRV)and transmissible gastroenteritis virus of swine(TGEV).There were 18 PEDV positive results in 20 samples of inspected feces and the detection rate was 90%.These18 positive samples could be used to study the characteristics of fecal microbiota in PEDV-infected piglets.In the 10 intestinal contents samples,4 samples were positive for rotavirus(RV)and the positive rate was 40%.Intestinal microbiota characteristics of piglets with diarrhea caused by PoRV were investigated with these RV positive samples.2.Through study the dynamic change of gut microbiota during porcine epidemic diarrhea virus infection in suckling piglets,we found that the abundance ofEscherichia-Shigella,Enterococcus,Fusobacterium and Veillonella increased due to dysbiosis induced by PEDV infection(P < 0.05).Notably,there was a remarkable age-related increase in Fusobacterium and Veillonella in diarrheal piglets(P < 0.05).Certain SCFA-producing bacteria,such as Ruminococcaceae_UCG-002,Butyricimonas and Alistipes,were shared by all healthy piglets,but were not identified in various age groups of diarrheal piglets.In addition,significant differences were observed between clusters of orthologous groups(COG)functional categories of healthy and PEDV-infected piglets.3.The comparative study of intestinal microbiota between 7-days healthy piglets and piglets infected with Rotavirus found that,Escherichia-shigella,Enterococcus and Staphylococcus are the dominant bacteria in the small intestinal of newborn piglets.And the abundance of these bacteria in the intestinal microbiota of PoRV-infected piglets is significantly reduced(P < 0.05).In particular,Lactobacillus amylovorus,Lactobacillus johnsonii and Lactobacillus salivarius,which have inhibitory effects on certain viruses,were extremely significantly increased in the disease group(P < 0.01).PoRV infection weakens or even disappears the correlation among some bacterial in the intestinal tract.Our research found that PoRV invasion altered the stability of the entire gut microbial ecological system in piglets,and also affected the intestinal function,particularly which function related to diarrhea.This study demonstrated that virus infection resulted in severe perturbations on the gut microbiota of piglets.Therefore,providing different supplements to suckling piglets at different ages according to the deficiency of beneficial bacteria at each age,may be a promising method for the prevention and treatment of viral diarrhea.