Structure And Function Of The Fecal Microbiota In Diarrheic Piglets And Association Between SLA-DQA Gene And Fecal Bacterial Community

Piglet diarrhea is one of the most common factors that affects the benefits of the swine industry,its effective prevention and control has been a focus of concern and research to producers.Many studies have shown that regulating the gut microbes was an efficient therapy for intestinal disease.Based on the important roles of gut microbiome on the development of piglet immune system and disease,Large White piglets were studied in this study,to investigate the dynamic distribution of fecal microbiota across different week-age in healthy piglets,differences of the fecal microbial diversity and composition between diarrheic and healthy piglets at different week-age,the fecal microbial function of neonatal diarrheic piglets,as well as the association between polymorphism of the SLA-DQA gene and fecal microbial composition of neonatal piglets,using 16 S r RNA gene sequencing and metagenomic sequencing.The major results are as follows:1.The fecal microbial diversity and major bacterial community of healthy piglets gradually changed with age and diet.The fecal microbial diversity of healthy piglets significantly depleted at 3-week old(after creep feeding),while significantly increased at 5-week old(after weaning).The genera Lactobacillus and Escherichia were the main fecal microbial communities of healthy piglets at 1-week old.The genera Bacteroides and Clostridium were the core fecal microbial communities of healthy piglets at 3-week age.And the genera Prevotella,[Prevotella] and Phascolarctobacterium as well as the family Veillonellaceae were the core fecal microbial communities of healthy weaned piglets at 5-week old.2.There were striking differences in microbial abundance between diarrheic and healthy piglets at different ages.1)Six phyla and fifteen genera as well as three phyla and twenty genera significantly differed in relative abundance of diarrheic and healthy piglets at 1-week and 3-week old,respectively.When comparing with the pre-weaning(1-week and 3-week old)healthy piglets,at phylum level,the relative abundance of the phylum Firmicutes was significantly decreased(P < 0.05),and the abundance of the phylum Fusobacteria was elevated in diarrheic piglets before weaning(P < 0.05).At genus level,Prevotella,[Prevotella],Sutterella and Anaerovibrio exhibited increased relative abundance in diarrheic piglets before weaning(P < 0.05),and the genera Escherichia,Clostridium,Ruminococcus and [Ruminococcus] exhibited decreased relative abundance in diarrheic piglets before weaning(P < 0.05).These results indicate that the increase in the abundances of Prevotella and [Prevotella],the concurrent decreases in Escherichia and the majority of beneficial bacteria that belong to the Firmicutes phylum,are associated with pre-weaning piglet diarrhea.2)One phylum and six genera significantly differed in relative abundance of diarrheic and healthy piglets at 5-week old.The phylum Spirochaetes as well as the genera Bacteroides,Clostridium,Ruminococcu,[Ruminococcus],Bulleidia,and Treponema exhibited decreased relative abundances in diarrheic piglets at 5-week old(P < 0.05).This indicates that decrease of the fecal microbes that helps digestion,absorption and assimilation of solid feeds is associated with post-weaning piglet diarrhea.3.Metagenome sequencing showed that 30 bacterial species were differential enrichments between neonatal diarrhiec and healthy piglets.Fusobacteria nucleatum,Fusobacteria necrophorum,and Prevotella spp.had higher relative abundances in neonatal diarrhiec piglets than those in healthy piglets(P < 0.01),while Escherichia coli,Bacteroides eggerthii,and the members of Firmicutes(e.g.Enterococcus faecium,Enterococcus faecalis,Lactobacillus spp.,Streptococcus spp.,Clostridium spp.,and Blautia wexlerae)had lower abundances in neonatal diarrhiec piglets than those in healthy piglets(P < 0.01).4.The microbial functional profiles in neonatal diarrheic piglets were significantly differed from those in neonatal healthy piglets.When comparing with neonatal healthy piglets,the differentially functional genes in diarrheic piglets were an significant increase in bacterial ribosome(P < 0.05),and significant decearse of the functional gene sets that related to vitamin biosynthesis,monosaccharide,amino acid and polyamine transports,as well as sugar-specific PTS transport,and two-component regulatory systems(P < 0.05).These profiles may impact the ability to transport and uptake nutrients,as well as fight microbial infections in piglet gut ecosystem,and thus are related to the development of neonatal piglet diarrhea.5.Polymorphism of the SLA-DQA gene was associated with the fecal microbial composition of neonatal piglets.A new nucleotide variation g.207C>A was detected in antigen peptide binding groove of the SLA-DQA,and allele DQA*03xa02 resulting from which was associated with the fecal microbial composition of neonatal piglets.Eight bacterial genera related to diarrhea were differed in relative abundance between 03xa02_presence and 03xa02_absence group piglets(P < 0.05).Relative abundances of the genera Prevotella,[Prevotella],Phascolarctobacterium,Anaerovibrio,Enterococcus,and Campylobacter were higher in piglets from 03xa02_absence group than those in piglets of 03xa02_presence group,the relative abundances of the genera Escherichia and Sutterella were lower in piglets of 03xa02_absence group than those in piglets of 03xa02_presence group,and Escherichia was negative correlated with the potential pathogens that related to inflammatory disease.These results suggest that intestinal protective E.coli increased and potential pathogenic bacteria decreased in piglets with the absence of DQA*03xa02.In summary,in diarrheic piglets,the abundances of Prevotella and [Prevotella] increased,E.coli and the majority of beneficial bacteria that belong to the phylum of Firmicutes decreased,the dysbiosis of these intestinal microbes are associated with the imbalance of energy metabolism and the weaking of immune function.Besides,polymorphism of the SLA-DQA gene was associated with microbial composition and neonatal piglet diarrhea.These results provide crucial references for the coming research on regulating piglet intestinal micro-ecological balance,preventing and treating piglet diarrhea.