Identification Of Gut Microbes Affecting Feed Efficiency And Feeding Behavior In Landrace Pigs Based On Microbiome

Feed efficiency and feeding behavior are important economic traits of commercial pigs,which are affected by host genetics,environment,intestinal microorganisms and other factors.In order to screen intestinal microbial markers related to feed efficiency and feeding behavior traits of Landrace pigs,this study determined phenotypic values of growth traits during the main fattening stage(90～160 days old)of 444 Landrace pigs,and collected 190 fecal samples of 90 days old(early fattening stage)for microbiome sequencing.Through the methods of intestinal microbial species composition analysis,alpha diversity analysis,beta diversity analysis,species difference analysis,correlation analysis and function prediction.Identify the intestinal microorganisms significantly associated with the feed efficiency and feeding behavior traits of Landrace pigs,in order to obtain the microbial markers related to the traits,so as to provide reference for the breeding and feeding management of Landrace pigs.The main research contents and results of this study are as follows:(1)The main rules of feeding behavior were analyzed in 444 Landrace pigs,and the following parameters were examined: feed conversion ratio(FCR),residual feed intake(RFI),average daily weight gain(ADG),average daily ad intake(ADFI),average per feed intake(FIV),average per feed TV,average daily TFD Non genetic factors and phenotypic correlations were performed for 9 traits:food intake rate(FR)and mean number of daily servings(NVD).Results showed little difference in feeding behavior traits between boars and sows,with more daily feed intake in boars than in sows.Sex was highly significant for RFI,FCR,and ADG(P<0.01);Climate had a significant effect on RFI,ADG,ADFI,and FR(P<0.05 or P<0.01).There was a high degree of positive correlation between FCR and RFI,ADFI(r=0.306～-0.713;ADG was significantly negatively correlated with FCR(r=-0.4/-0.279),significantly positively correlated with FIV and FR(r=0.266～-0.49),and not significantly correlated with RFI.Feed efficiency traits were more strongly correlated with feeding behavior traits in boars than in sows.(2)The fecal microorganisms of 190(111 sows,79 boars)90 day old Landrace pigs were subjected to 16 S rRNA gene high-throughput sequencing analysis.Analysis of environmental factors affecting the gut microbiota found that column location,climate,open test day age and open test weight had a large effect on the data distribution of gut microbiota samples.Enterotype identification showed that two enterotypes,Streptococcus enterotype and Gemmiger enterotype,existed in the fecal microbiota of 90 day old Landrace pigs,and enterotype significantly influenced ADG(P<0.05),and enterotype clustering was not affected by sex and climate.Analysis of differencest genders in the composition of the gut microbiota composition between boars and sows revealed highly significant differences between genders.(3)Based on the sequencing results and phenotype data of the gut microbiota from above 190 individuals,we used several microbiome analysis methods,including group difference analysis,lefse(LDA effect size)analysis,random forest analysis,and correlation analysis,to identify and screen gut microbes associated with 9 feeding efficiency and feeding behavior traits in Landrace pigs.Based on the overlapping results of two or more analytical methods combined with the microbial functions that have been previously studied,we found that the following gut microbes significantly and positively correlated with feed efficiency and feeding behavior traits in Landrace pigs were dominated by Subdoligranulum,Azospirillum,Faecalibacterium,Gemmiger,Roseburia,Peptococcus,Collinsella,Clostridiaceae＿Clostridium(TFD and NVD)and Butyricicoccus,etc,were the predominant gut microbes significantly positively correlated with feed efficiency and feeding behavior traits in Landrace Pigs.The significantly negatively correlated gut microbes were Clostridiaceae＿Clostridium,Peptostreptococcaceae＿[Clostridium],SMB53,02d06,CF231,Corynebacterium,Peptococcus,p-75-a5,Dehalobacterium,Dialister,Fusobacterium,Oscillospira,Coprococcus and Streptococcus.The above genus level microbes may serve as potential gut microbial markers associated with feed efficiency and feeding behavior traits in Landrace pigs.(4)To further mine the gut microbial species and metabolic pathways associated with the feed efficiency and feeding behavior traits of Landrace pigs,the fecal samples from a total of 30 individuals(14 sows and 16 boars)in the high and low groups for FCR/RFI and ADFI were selected from the Landrace population for metagenomic sequencing analysis.Sequencing of the feces of 30 Landrace pigs obtained a total number of reads of 12 6536 3144,with an average number of 4217 8771.Base sequencing quality Q30 ≥ 93.8,which indicated this sequencing quality qualified.After quality control,the average number of total effective sequence bases was 62 9548 1473,and 403 2510 contigs were sequenced after splicing,the average number was 13 4417.Based on the results of 16 S rRNA sequencing analysis,metagenomic sequencing analysis was used to further identify 107 species that were significantly associated with FCR/RFI in Landrace pigs,mainly from the Clostridium,Corynebacterium,Dialister,Bifidobacterium,Treponema,Aeromonas and Faecalibacterium,Among them,Corynebacterium sp.2039 was also significantly and negatively correlated with feed efficiency and average daily feed intake traits,which may serve as a potential marker species for feed efficiency traits.Among the functional pathways,the differential pathways mainly enriched in the high feed efficiency(LFCR)group and the low ADFI group were carbohydrate metabolism,other glycan biodegradation,and amino acid metabolism,among other pathways.The differential pathways mainly enriched in the low feed efficiency(HFCR)group were membrane transport,terpenoid and polyketide metabolism,and other pathways.The differential pathways mainly enriched in the high average daily intake group(HADFI)were lipid metabolism(fatty acid biosynthesis),Biosynthesis of various secondary metabolites and other pathways.In summary,in this study,we used 16 S rRNA sequencing and metagenomic sequencing to investigate FCR,RFI,ADG,ADFI,FIV,TV,TFD,FR,and NVD in Landrace pigs through a variety of analytical methods to mine the key microbes that affect the feed efficiency and feeding behavior traits,such as Corynebacterium,Bifidobacterium,Treponema,Dialister Faecalibacterium,Subdoligranulum,and Gemmiger,etc;Analysis of relevant microbial functional pathways found that high feed efficiency group was similar to low average daily feed intake group.They are mainly focused on carbohydrate metabolism,other glycan degradation,and amino acid metabolism pathways.Because the high feed efficiency group probably can meet the nutrient requirements for growth with relatively less feed.Gut microbes may play a role in regulating nutrient absorption,energy metabolism and appetite control.The results of this study provide a reference for further validation of the functional mechanisms by which the gut microbiota affects feed efficiency and feeding behavior in pigs,and provide a theoretical basis for developing the use of microbes to regulate the growth and health levels of pigs.