Analysis Of Intestinal Microbiota And Partial Bacterial Isolation Identification In Weaned Goats

The intestinal flora is closely related to the host’s physiological processes such as growth and development,nutritional metabolism and immune regulation.The dynamic relationship between the intestinal flora and the host is beneficial to the host’s life activities,but the organism can also suffer from diseases caused by the dysbiosis of the intestinal flora..Weaning is an important part of goats farming,and changes in feed and weaning stress are important factors that affect the intestinal flora of goats.Therefore,it is important to study the composition and changes of the intestinal flora of goats during weaning period for healthy growth and development of goats..1.Composition and development of the intestinal flora of healthy weaned goatsA total of 12 faecal samples were collected aseptically from 45-day-old weaned goats at 0,5,10,20,30 and 45 days after weaning,and sequenced by macrogenome sequencing technology.The Firmicutes and Bacteroidetes are the absolute dominant microflora in the post-weaning goats gut,with a combined relative abundance of 84%～91%.Clostridium,Prevotella,Faecalibacterium,Ruminococcus,Bacteroides and Parabacteroides are the dominant genus in the intestinal tract of weaned goats.The dominant flora showed dynamic changes in the composition of the intestinal tract of weaned goats at different ages,with the relative abundance of Bacteroides decreasing significantly from day 0(56.30%)to day 5(41.71%)of weaning,then showing an increasing trend and reaching the highest relative abundance at day 30(72.9%)of weaning;the changes of Bacteroides showed an opposite trend to those of Firmicutes,with the highest abundance at day 5(46.75%)of weaning,and the highest abundance at day 5(46.75%)of weaning.The relative abundance of Bacteroidetes was highest at day 5(46.75%)and lowest at 30 days after weaning(16.49%).A comparative analysis of multiple samples showed that the number of species in the intestinal tract of lambs was significantly lower on day 5 than on other days of weaning,and the main coordinate analysis showed that the structure of the intestinal microflora of goats on day 5 differed significantly from that of goats on other days of weaning,possibly due to a transient disturbance of the intestinal flora caused by external stress or stimulation.2.Composition and analysis of the intestinal flora of weaned goasts with diarrheaA total of 10 faecal samples from weaned gosats with diarrhea were collected aseptically and analyzed by matagenome sequencing technology,showing that 58 phylum,80 orders,95 classes,266 families,599 genus and 2480 species were annotated in the 10 samples.At the phylum level,Firmicutes was the highest relative abundance of microorganisms in the intestinal tract of diarrheic weaned goats,followed by Bacteroidetes and Proteobacteria.The dominant genus in the intestinal tract of diarrheic goats varied,with Escherichia,Bacteroidetes,Clostridium and Ruminococcus being the dominant genus respectively.In addition,opportunistic pathogenic genus such as Staphylococcus,Shigella and Mycoplasma are represented in the microbial composition of the intestinal tract of weaned goats with diarrhea.Among the 113 opportunistic pathogenic bacteria screened in the microbiological composition of the intestine of diarrheic goats,the relative abundance of Staphylococcus aureus,Escherichia coli,Shigella sonnei,Helicobacter pylori and Klebsiella pneumoniae in the intestine of diarrheic weaned goats was high.A comparative analysis of the microbial composition of the intestinal tracts of weaned goats with diarrhea at a similar age and healthy goats showed that there were differences in five phylum,six families and 26 genus,with the relative abundance of the Proteobacteria being significantly higher(P<0.05)and that of the Spirochaetes and Fusobacteria being significantly lower(P<0.05)in the intestinal tracts of diarrhea-weaned goats.At the family level,the relative abundance of Enterobacteriaceae was significantly higher(P<0.05)and that of Ruminococcaceae,Eubacteriaceae and Spirochaetaceae was significantly lower(P<0.05);at the genus level,the relative abundance of Escherichia,Helicobacter and Shigella were significantly more abundance(P<0.05),while Ruminococcus,Eubacterium,Treponema,Butyrivibrio,Fibrobacterium and Treponema were significantly less abundant(P<0.05).Butyrivibrio,and Fibrobacter were significantly lower in relative abundance(P<0.05);at the species level,the relative abundance of a total of 10 pathogenic bacteria,including Staphylococcus aureus,Escherichia coli,and Shigella sonnei,was higher in the intestine of diarrheic goats than in healthy goats,whereas a total of 10 species,such as Treponema bryantii,Prevotella ruminicola,Ruminococcus flavefaciens and,Ruminococcus_bromii,Desulfovibrio,the relative abundance of probiotics in the intestinal tract of weaned goats with diarrhea was significantly reduced.The above results suggest that the growth and multiplication of various pathogenic bacteria in the intestinal tract of weaned goats and the reduction of probiotics may be one of the important causes of diarrhea in weaned goats.3 Isolation and identification of intestinal bacteria from weaned goatsPost-weaning goats faecal samples were collected and the bacteria were isolated and cultured using common media for intestinal probiotics such as BHI,YCFA,PYG,M2GSC,MRS,CDC agar and EG agar.63 strains of intestinal probiotics or potential probiotics were obtained.Further identification showed that these bacteria belonged to 17 species in 9 genus of 7 families.These included Bacteroides uniformis,Bacteroides fragilis,Bacteroides xylanisolvens,Bacteroides rodentium,Bacteroides thetaiotaomycetes,and Parabacteroides merdae,Enterococcus hirae,Bacillus subtilis,Bacillus pumilus,and Bacillus cereus.Bacillus safensis,Lactobacillus acidophilus,Lactobacillus amylovorus,Limosilactobacillus reuteri,Pediococcus pentosaceus,Bifidobacterium pseudolongum,Proteiniclasticum ruminis,etc.This will provide a rich source of strains for subsequent research on probiotics and the development of probiotic formulations.4 Isolation and identification of intestinal pathogenic bacteria from weaned goatsFecal samples were collected from healthy and diarrheic weaned meat sheep and a total of 45 pathogenic and conditionally pathogenic strains belonging to 23 species in 16 genus and 11 families were isolated and identified by common and selective culture methods combined with bacterial 16S rDNA sequencing,induing casseliflavus、Vagococcus carniphilus、Vagococcus teuberi、Escherichia coli、Citrobacter farmeri、Comamonas kerstersii、Acidovorax.sp、Fundicoccus fermenti、Fundicoccus ignavus Acinetobacter tandoii、Acinetobacter lwoffii、Proteus mirabilis、Providencia rettgeri Aeromonas hydrophila、Aeromonas caviae、Aeromonas enteropelogenes、Clostridium perfringens、Staphylococcus simulans、Sanguibacter.sp、Jeotgalibaca ciconiae、Staphylococcus aureus and Shigella flexneri.As Staphylococcus aureus and Shigella flexneri are closely associated with diarrhoea in weaned meat sheep,drug susceptibility analysis was carried out focusing on Staphylococcus aureus and isolated The results showed that all five strains of Staphylococcus aureus were sensitive to levofloxacin,amikacin and gentamicin,and resistant to ampicillin and piperacillin,while three strains of Shigella flexneri were resistant to tetracycline and sensitive to levofloxacin,ciprofloxacin,amikacin and gentamicin.