Detection And Analysis Of Gut Microbiome And The Effect Of Antibiotic Treatment On Diarrhea Lambs

In the modern sheep breeding process,probability of diarrhea in lambs is always high.Diarrhea seriously affect the growth and survival of lambs.The use of antibiotics to treat diarrhea in lambs is currently the most common treatment,but can have serious effects on the animal’s gut microbiome.In order to explore the changes in the gut microbiota of lambs with diarrhea and the effect of antibiotic treatment on the gut microbiota of lambs,16 S r RNA gene sequencing technology and metagenome sequencing technology were used to provide theoretical basis for sequencing pathogenic bacteria of diarrhea lamb,to screen out pathogenic bacteria and probiotics that can cause diarrhea of lambs.Six healthy Tan sheep lambs and six diarrhea Tan lambs(2-3 month-old;22 ± 3 kg,half male and half female)were selected,and anal swabs were collected,and the samples were recorded as the healthy group(group H)and the diarrhea group(group D).The lambs in group D were treated with 3 m L of antibiotics(florfenicol)daily until the lambs returned to health,marked as rehabilitation group(group R)and then sequencing the feces again.Collected feces for 16 S r RNA gene sequencing analysis changes in microbial abundance and structure.Chose three lambs from each group for metagenome sequencing to analyze the changes and differences in gut microbial species and functions.The test results are as follows:(1)Simpson and Sobs indices of intestinal microbial alpha diversity in diarrhea group(group D)were significantly lower than that in healthy group(group H),and the beta diversity was extremely significantly different(P<0.01).At the phylum level,the relative abundances of Proteobacteria and Fusobacterium were significantly increased(P<0.05),and the abundance of Bacteroidetes was significantly decreased(P<0.05)in the F group.At the genus level,the relative abundance of Escherichia coli-Shigella was extremely significantly increased(P<0.01)and the relative abundance of Turicibacter increased significantly(P<0.05)were the main cause of diarrhea of lambs in this experiment.(2)The results of metagenome sequencing showed that diarrhea had no significant effect on the community structure of Eukaryota and Archaea in the gut,and there was no significant difference in the KEGG pathway between the two groups.The content and relative abundance of carbohydrate active enzymes decreased in diarrhea group.Tetracycline and bacitracin resistance genes were widespread in both groups,and the abundance of antibiotic resistance genes in diarrhea group was higher than that in healthy group.(3)The intestinal microbial composition of the rehabilitation group(group R)was significantly different from that of the healthy group and the diarrhea group(P<0.01),and the microbial diversity and richness were significantly lower than those of the diarrhea group(P<0.05).At the phylum level,the relative abundance of Bacteroidota decreased significantly(P<0.01),and the relative abundance of Verrucomicrobia decreased significantly(P<0.05);the relative abundance of Proteobacteria remained the same Significantly higher than the healthy group(P<0.05).At the genus level,the relative abundance of Clostridium＿innocuum＿group and OTU858 in Ruminococcus was significantly increased(P<0.05),and the increased trends of the relative abundance of Lactobacillus and Butyricicoccus,was speculated to be potential probiotics that modulate gut microbiota in lambs with diarrhea.In conclusion,the gut microbial diversity and richness of lambs with diarrhea were significantly decreased.The relative abundance of Escherichia coli-Shigella and Turicibacter was significantly increased,which may be an important cause of diarrhea in lambs.The content and abundance of carbohydrate enzymes in the intestines of lambs with diarrhea decreased,and the abundance of antibiotic resistance genes was higher than that of the healthy group.Antibiotic treatment significantly reduced the relative abundance of Bacteroidota(P<0.01),decreased the relative abundance of pathogenic bacteria Turicibacter(P<0.05).The relative abundance of Escherichia coli-Shigella did not change significantly.The relative abundance of Clostridium＿innocuum＿group,Ruminococcus＿torques＿group,Lactobacillus and Butyricicoccus tended to increase is an important factor in regulating the intestinal flora of lambs with diarrhea.